File Systems

navigating and managing a structured organization

In What's a Computer? we told you about temporary and permanent storage devices.  Following are general details about the file systems of permanent storage devices.

Though considerably more complex, your computer's file system is a bit like your desk - it's a heirarchy of containers.  To carry the analogy further, the operating system manages file systems somewhat like you manage your desk (more accurately perhaps, but certainly with less flair).

When you first enter the room and look at your desk, the part you first notice is the desktop - assuming you can even see it (desktop jokes are so tempting).  Likewise, when the computer is running, the entire display area of your monitor, behind any open windows, is called the "Desktop".  In the file system, the Desktop also appears as the outer, or top level, container of all else.

Here, you may wish to open Windows Explorer and follow along.  Right click My Computer, then click Explore in the context menu.  Or click Start, then hover the pointer over Programs, then Accessories, then System Tools, and then click Windows Explorer.

Windows Explorer displays two panes.  The lefthand pane lists container objects ("folders") in heirarchical order.  (If instead you see a list of tasks, click the Folders button on the toolbar.)  By clicking the small box, marked with a plus or minus sign, to the left of a container object, you can display or hide that object's inner containers, if any, in the lefthand pane.

If you click a container object's icon or name in the lefthand pane, the righthand pane lists the container's contents, if any, including inner containers and/or files.

Within the Desktop, among other things, is a large container called My Computer.  Within My computer, among other things, are containers called logical drives (or simply "drives") which are uniquely identified by a drive letter from "A:" to "Z:" (including the colon character).

These are permanent storage devices, and may include internal and external hard drives, optical drives, flash drives, cardreader drives, tape drives, and network drives (which exist on other computers).

While different types of drives have their own different file systems, or support more than one, modern computers integrate the management of those file systems to present you with relatively consistent operating characteristics; i.e., they all appear to work pretty much the same, with a few differences.

Within drives are containers called folders, which may contain subfolders - much as your desk contains drawers, which in turn may contain boxes of candy hidden among folders - and files.  The drive itself is also treated as a folder called the "root folder", or "drive root".

Finally, folders contain files.  Files are containers as well - they may contain data, controls, program code, and references to other containers - but they are called "noncontainer objects" because they do not hold other containers, only data.


In light of what you've just read about the file system heirarchy, a "fully qualified file specification", or "filespec" - a description of the file's name and location - looks like this:

"drive:\path\fn.ext",  where:

drive:    is a single drive letter followed by a colon.  Example:  "C:".  As the root folder, the drive is followed by a backslash.
path\    includes all nested folders, if any.  Each is followed by a backslash.  Example:  "parent\child\etc\".  If the file is in the drive root, the filespec is just "drive:\fn.ext".  Note that Internet browsers use forward slashes ("/") instead of backslashes.
fn    is the file's arbitrary name, or "filename".  Often the entire "fn.ext" is also called a filename, however:
.ext    is the file's "extension" (or "filetype"), if any, preceded by a period.  While some are arbitrary, others are reserved for files with specific properties and are associated with specific programs.  Example: by default, double clicking a "fn.txt" file causes it to be opened by a text editing program named "Notepad.exe".  You can look up the meaning of standard extensions at

By default, a Windows setting hides file extensions, so a file named "MyFile.txt" and another named "MyFile.doc" appear simply as "MyFile" and "MyFile".  To eliminate this unnecessary confusion and decrease your opportunity for error:

open My Computer > Control Panel, or open Windows Explorer > Tools.  Then open Folder Options > View tab.  Scroll down the Advanced Settings list, and uncheck Hide Extensions For Known Filetypes.

While you're there, make sure that Hide Protected Operating System Files is checked!  Then click OK.


Computers have a "system drive":  a hard drive partition which is specially dedicated to hosting the computer's operating system.  Proper functioning, also called the "health", of this drive is critical to the computer's well being.

Since this well being is first priority, we'll focus on the most common workhorse - the hard drive.

A standard hard drive contains a disk made of magnetic material and a pivoting armature with "heads" which can read from and write to the disk.  In operation, the disk spins on a central axis while the armature moves back and forth, reading and writing data.

Each hard drive has its own fixed spin rate, typically in the range of 4800 to 7200 rpm (that's 120 revolutions per second), and the armature rapidly sweeps at less than a hair's breadth over the surface of the disk.  Therefore, you should not move a hard drive while it's running.

A hard drive's most common enemies are:

Corruption:  usually the result of circumventing the system's built in protections through improper settings or bad software.  Except for viruses, corruption causes some of the more difficult problems commonly found.  Its effects, best described as distortions, can be anything including garbled or missing data, files, folders, even drives, and system instability and crashes.  Usually, but not always, Windows will mark the drive as "dirty" and tell you to clean the drive with the "ChkDsk" or "ScanDisk" program.  In a properly maintained system, corruption is rare.

Fragmentation:  When a file is written to disk, Windows writes fragments of that file wherever they will fit.  Over time and without proper maintenance, you could easily have hundreds of files in thousands of fragments.  This doesn't hurt your system directly but, for the task at hand, it has to work harder to disregard all the fragments that aren't needed, and to find, organize, and assemble the fragments which are needed, every time they're needed.  Windows doesn't gripe about this at all, it just works harder and runs slower.  Then you gripe.  Instead, run the Disk Defragmenter periodically.

To maximize your hard drive's performance and reliability, get a copy of Diskeeper® — prevent disk fragmentation while you work.

Time:  Actually we mean the total amount of movement that the drive's parts have endured.  Moving parts gradually wear out; however, unless the drive is always working hard and/or constantly overheated, it should last a very long time.  Modern hard drives normally give you your money's worth and more.


A physical drive is partitioned into one or more logical drives, each with its own drive letter.  The first created (or only) partition is called the "primary partition".

Your default (or only) operating system is installed on the primary partition of a physical drive inside the computer.  This partition is marked as the "Active partition" so the computer recognizes it as the system drive.  On PC computers, this is typically drive C:.  (Note that drive letters A: and B: are reserved for floppy disk drives.)

Unless otherwise noted, the following information assumes a default installation of the Windows operating system on a PC computer.


Among other items on the system drive is a set of specialized folders created when Windows is installed.  Briefly, these are:

C:\Documents and Settings

This folder contains a "profile" subfolder for each user account on the system, an additional profile which applies to All Users, and optionally a Default User profile which can be tailored to simplify the creation of new user accounts.

Creating, removing, or renaming a user profile must be performed only through the User Accounts control panel.  Never attempt to manipulate these outer profile folders by any other means.

As a general rule, do not alter any of the subfolders within a profile.  Many of these subfolders have specialized properties and functions, such as the user's Desktop and Start Menu, which may be corrupted or destroyed by tinkering with them.  Other folders contain data or provide a work space which directly affects the proper operation of various applications.

That being said, there are some subfolders and files, further down in the folder heirarchy, which you can (and will) freely alter, such as the contents within:

"C:\Documents and Settings\username\Favorites\...", and

"C:\Documents and Settings\username\My Documents\..."

C:\Program Files

This folder contains installed software other than the Windows operating system, and provides a common ground for sharing some components among various applications.

Ideally, adding, removing, or changing the contents of this folder (and its subfolders) is handled through software installers or uninstallers, the Add/Remove Programs control panel, or by normal settings and operations of the installed software.


This folder contains the Windows operating system.  Its contents are managed by Windows Update and the operating system itself.

Do not add, remove, or change anything within this folder or its subfolders without a clearly defined reason for doing so and complete instructions from a trusted source.

With this brief description and list of 'no-no's, we have barely scratched the surface of the file system and the standard Windows folders in order to prepare you for more specific information in our Trade Secrets.


Now let's focus on some basic methods for working with the file system.  While there are more complex ways to accomplish the same tasks, some of the following instructions require the use of a mouse which has at least two buttons (with apologies to users of Apple's Cyclops mouse).

According to the default settings, quickly pressing and releasing the large lefthand mouse button once is called a "click", while the same action with the large righthand button is called a "right click".  Pressing and releasing the lefthand button twice in rapid succession is called a "double click".

If you are left-handed, note that you can reverse the definitions of these two mouse buttons through the Mouse control panel.  If you do, you will need to make an opposite interpretation of all references to the left and right mouse buttons.

Depending on the location of the mouse pointer, a right click usually opens a "context menu" which provides options appropriate to the context.  For example, right clicking a file will open a menu of actions appropriate to files, such as Open, Copy, and Delete.

If you don't already have one, let's now create a "sandbox" where you can safely play.  If you are new to this, we recommend creating a new folder within one of three locations:

"C:\Documents and Settings\username\My Documents",

the root folder "C:\" (if you have permission), or

on the Desktop (so you can skip some of the navigation)

If using a folder, open it in Windows Explorer and right click an empty area in the righthand pane.  If using the Desktop, just minimize or close any open windows to get them out of the way, and right click an empty area on the Desktop.

In the context menu, point to New, then click Folder to create a new folder.  The instant it is created, it is also ready to be renamed unless you first click somewhere else or hit the Enter key - if you did, just click the new folder, then wait a second, then click it again to enable renaming (its filename box changes color to indicate it is selected).

Now type a new filename for this folder - let's call it "sandbox" (without the quotes) - then press the Enter key.  Note that folders and files can only be named from a limited character set.  If you attempt to use illegal characters, Windows will gripe and remove them.

Now let's create a new file in the same location (outside of the sandbox folder), using a similar procedure.  Right click an empty area, then point to New, then click Text Document in the context menu to create a new text file.  Then rename it to "sand.txt".

To "drag" an object, such as a file or folder, to a new location, hover the mouse pointer over the object, then press and hold down the left button, then move the pointer to the new location.  To "drop" the object into the new location, release the left mouse button.

This whole procedure is called "drag and drop".  Now you can try it yourself:  use drag and drop to put sand.txt into your sandbox.  Notes:

The tip (or "hot spot") of the mouse pointer, rather than the picture of the object you are moving, must be directly over the new location when you drop the object.

If the new location is a folder, wait briefly for the folder to be automatically selected (its icon changes color) before you drop the object.

If the new location is a menu of cascading folders, like some toolbars, the Start Menu, and folders in the lefthand pane of Windows Explorer, wait for the first folder to open, then move the pointer through the cascading folders until you find your target folder (remember, you're still holding down the left mouse button), then drop the object.

If the new location is on another logical drive, drag and drop performs a Copy, rather than a Move operation, so a copy of the file remains at the old location.  For greater control, drag and drop using the righthand mouse button instead of the left.  Then when you drop the object, a context menu appears with options to Copy or Move the object, to Create a Shortcut for it at the new location, or to Cancel the operation.

If you drop the object onto a program icon, the object is not moved; instead you are asking the program to process the object.  Example:  If you drop a text file on the icon for Notepad.exe, Notepad will open the file for editing.

If the mouse pointer changes to a small icon which looks like the universal "NO" symbol (a circle with a slash through it), then you cannot drop the object into that location.

If you want to cancel the action of dragging with the left mouse button, move the object back to its old location, and drop it.  If Windows gripes about this, respond appropriately.

If you made a mistake and you can't figure out where you dropped the object, immediately right-click an empty area of the Desktop or the righthand pane of Windows Explorer, and click Undo Move in the context menu to put the object back in its old location.

Don't use the Undo functions carelessly.  They simply undo the most recent related action, regardless of what caused it, where it occurred, and when.  You may inadvertently cause problems if you Undo a Move or Rename action which was purposely executed by a software update or other operation.

Goof-proof Renaming

Windows permits long filenames which can be used to advantage for quickly recognizing file contents.  Let's say you have a file in your system Change Log folder with a complex name like:

20080413-2356 Installed Diskeeper 2008Pro update v12,0,781,0.txt

and you now notice that you typed the wrong date or version number and wish to correct it.  You need to click it twice, slowly, to make it ready to rename.

Then, because the entire filename (including the extension) is selected, you need to either click once again inside the filename box, or press the Home or End key so that the filename is deselected.  Otherwise, the next character that you type will replace the entire filename.

If this happens:

Method 1:  Stop immediately - do not click elsewhere or press the Enter key.  Now delete all characters, including spaces, from the filename, until the text cursor does not move when you separately press the Home and End keys.  Now press the Enter key to retrieve the old filename.  This works because Windows does not permit you to assign a null (empty) filename.

Method 2:  If you have already replaced and confirmed the accidental filename, immediately right click an empty area in a folder or on the Desktop, then click Undo Rename in the context menu.  This method is less precise than Method 1 because it simply reverses the most recent rename operation, regardless of what caused it, where it occurred, and when.

While drag and drop can be useful, it also involves extra risk - partially due to the stress of holding down a button, while carefully positioning the mouse pointer, while watching for and interpreting clues.

To Copy or Move objects with the highest degree of control and precision and the greatest of ease, use the Copy, Cut, and Paste actions in the context menus:

To Copy:  right click the object, then click Copy.  Open the new location and right click an empty area inside it, then click Paste.

To Move:  right click the object, then click Cut.  Open the new location and right click an empty area inside it, then click Paste.  Note that the object is removed from its old location only after Windows creates and verifies a copy of it at the new location.

To Create a Shortcut:  right click the object, then click Copy.  Open the new location and right click an empty area inside it, then click Paste Shortcut.

Why create a shortcut?  Efficient organization suggests that you place one copy of original files of a specific kind in one location - a designated folder.  For example, you might store all office accounting files in "C:\Office\Accounts\...".  Now suppose you need to view or edit one of those files frequently and quickly:

Method 1:  Copy the file to your Desktop.  Now the same data occupies twice as much disk space.  Soon, you can easily lose track of what changes were made to which file.  This in turn can cause minor to serious business problems (or computer problems, if you're working with system control files).

Method 2:  Create a shortcut to that file on your Desktop.  The shortcut is tiny, occupying about 1KB.  When you double click that shortcut, it opens the original file at its original location.  Make sure you have good backups, and you're set.  If you no longer need the instant access, just delete the shortcut - the original file remains intact.

While we're on the subject ...  If you have any shortcuts on the Desktop to the contents of slower drives such as flash drives, optical drives, or worse, floppy drives, you can improve system response time by removing those shortcuts.

Depending on current events, the system can "refresh" the Desktop quite often.  Every time it does, it re-verifies the targets of those shortcuts.  This includes interrogating the target drive's file system and waiting for a response.  Slower drives can take quite a while to respond.

Therefore a collection of such shortcuts can slow a single refresh down to a crawl - the Desktop goes partially or completely blank and then each element reappears, one ... by ... one.  At least you can amuse yourself by watching the drive activity lights.

(If you're not actively using the system, yet the system drive's light shows constant activity, see our other Trade Secrets page about memory management and optimization.)

In any case, you should avoid dropping a lot of stuff on your Desktop.  While it's very useful for very short term items, a dense long term clutter degrades response time and your sanity.

For a quick solution to this, create a folder on your Desktop and name it "DROP".  Then ruthlessly drag and drop all nonessential icons into it.  Do not move icons for system folders, such as Internet Explorer, My Computer, My Documents, My Network Places, and Recycle Bin, from the Desktop.

To verify these, open Windows Explorer, click the topmost Desktop folder in the lefthand pane, and review its contents in the righthand pane.  If the "Type" column identifies an object as a System Folder, don't move it.  If in doubt, don't move it.

A common source of clutter and confusion is creating duplicate shortcuts, shortcuts for other shortcuts, and shortcuts on the Desktop for items which are already on the Desktop.


You should consider coordinating your personal folders with your backup plan, including the available space on your backup media.  For example, you could create three major folders:

to contain smaller, critical files which should be backed up frequently on small portable media such as optical disks, flash drives, or micro hard drives.

to contain general work files, documentation, and references which need to be backed up less frequently on mid-sized media such as micro or regular hard drives.

to contain large archival and media files (audio, graphics, and movies) which only need to be backed up occasionally on large hard drives.

Ideally, the total size of each folder's contents will not exceed ¾ of the capacity of the backup media.  We encourage you to use external media, including USB connected hard drives, so your data will be safe in the event of catastrophic system failure.

We also encourage you to keep your system drive as clean as possible.  If you have other partitions on the same physical drive or, better yet, another physical hard drive inside the computer, these are the best places to store your data - and your backups, if you have no external media.

You can also relieve stress on your system drive by installing programs to other partitions on internal hard drives.  While there is no serious danger in doing so, we generally recommend that you avoid installing programs on external media.  Critical items, such as your browser and security software, should only be installed on your system drive.

now reading: File Systems - Explore, Manage, Protect
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