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Here is a post I saved from Train:

Previously posted by Train:
Programs running in background For whom who asked the original question. I think you need a little more information, because you may be trying to defrag without having done a few other necessary steps first. Which could explain why it is taking so long. Defragging should really be a third step after:
(1) deleting unnecessary files from your computer (what's the point of rearranging useless files?) and
(2) running the computer through a scandisk -[ which checks the surface for damaged sectors only when run in the thorough/ surface scan so that files are not put there in the defrag process.]
I wrote the following notes for colleagues at work, who knew nothing about disk maintenance, based on information gleaned from a number of websites and books. I hope you can get some benefit from them as well.

Step 1: Deleting Folders and Files
A. Folders on the C drive from which all files can safely be deleted:
-> Windows \ Temporary Internet Files {deletes cookies including website log in info / payed to surf cookies if done using Windows explorer}[Deltree this directory from DOS does not effect cookies]
-> Windows \ Downloaded Program Files {contains files you may want to leave alone. Java, Activex applets that will be downloaded again when you visit the site again, addding time to load webpage. And windows Update site uses applets stored here.
-> Windows \ History
-> Windows \ Temp
-> Windows \ Cookies [Again payed to surf need these and Login cookies are here also.]
-> Windows \ Favorites (all can be deleted if you do not use Internet Explorer as your browser)
The simplest way to delete all files in a folder is to highlight the folder in Windows Explorer, click the menu item EDIT>SELECT ALL, then hit the DELETE key.
B. Files (but NOT personal files) that can be deleted are selected on the basis of their extension i.e. the three letters that appear after the 'dot' and file name.
Files which can be safely deleted are found in three places:
-> in Windows Explorer
-> in email mailboxes
-> in your browser (e.g Netscape or Internet Explorer)
Windows Explorer
In Windows Explorer, any file can be found by going to the menu item TOOLS>FIND>FILES OR FOLDERS. In the dialog box, type *.xxx, where xxx is the file type (listed below). The file types can be entered one at a time, or several at once, separated by semi-colons, for example *.gid; *.cnt. Specify the drive to look in (usually C), make sure the INCLUDE SUBFOLDERS box is checked, then FIND NOW. Note (1): The * is a 'wild card' and will allow all files with that extension to be found, irrespective of file name. Note (2): If you have any concerns about deleting a file, create a temporary folder (perhaps under 'My Documents') named DELyymmdd, where yymmdd is the current year, month and day. Move the files you are not sure about deleting to this folder, and if after experiencing no adverse effects for a week / month (depending on computer use) then delete the folder and its contents. File types which can be deleted, and what they are:
*.gid, *.cnt, *.ftg, *.ann, *.bmk
These files are Help sections, and will regenerate when needed.
*.avi, *.fts, *.diz, *.tmp, These files include How-To animations, files created when you do a search in a Help file, lists of files on previously installed programs, and temporary or old version of files. *.~??, *.??~, *.bk2, *.001, *.002 through to *.999 (with the exception of *.386)
These are also temporary files
*.wav, *.mid
These are sound files, and you may want to keep them (say for PowerPoint). Most are junk
Delete these files after extracting the program files from them. If you feel unsure doing this,or want to, save the files to clearly labelled floppy disk, cd, zip or ??*.chk located directly on the C drive (C:\*.chk) but NOT those in any regular program folders
They are the result of running ScanDisk Mscreate.dir and/or a folder called ~Mssetup.tUnder the Windows Explorer menu VIEW>OPTIONS>VIEW, make sure the SHOW ALL FILES option is checked. Search the entire C drive for these two files and delete them. They are empty files created by Microsoft installation programs.
Because each email program is different, I will not try to give instructions on how to clean these up, but I am sure if you check your IN and OUT boxes, you will see which files can either be deleted forever, or zipped up and stored on floppy or another backup utility.
This is the browser I use, so this is why I can provide instructions for it. If you use IE or any other browser, someone else can provide the relevant details.
If you use Netscape to browse the internet, there is a lot of junk retained after each visit. To clear it out, go to the Netscape menu item EDIT>PREFERENCES. In the dialog box that comes up, click on Category>Navigator. On the RHS of the dialog box, under the section 'History Box', click on the button 'Clear History'. In the section beneath 'Location Bar History', click on the button 'Clear Location Box'. Click on the Category>Advanced>Cache menu, and clear the Memory Cache and the Disk Cache.
The next step is absolutely vital!
Step 2: ScanDisk
This program is built in to Windows and is designed to check for errors on the surface of your hard disk ('bad sectors') and errors in the files and folders, many of which ScanDisk can also fix. To make ScanDisk run at its best, no other programs should be running at the same time, and must be closed down. Many people do not realise that as well as the programs you choose to open yourself, a number of programs start automatically when you turn on your computer. These must also be closed down BEFORE you run ScanDisk. How do you know what is open? Pressing the three keys Control, Alt and Delete at the same time (C/A/D) will bring up a list of the programs running in the background of your computer. Not all programs should be turned off, otherwise the computer will not run at all. The two programs which MUST BE LEFT RUNNING are Explorer and Systray, all others can be closed down (one at a time) by pressing C/A/D, and choosing End Task. You may not recognise what some of these programs are, but invariably will include your virus checker - there may be several of these, checking incoming email, a random virus scan at startup, as well as continuous background scanning.
There may also be an MS Office toolbar. There is one other step to do before starting ScanDisk. You must turn off any screen savers. To do this, either go to Start>Settings>Control Panel, and open Display, OR right click on the desktop and choose Properties. You will get several tabs: click on Background, and set wallpaper to NONE, click on the Screen Saver tab and also set to NONE. To start the scan, Go to Start>Programs>Accessories>System Tools>ScanDisk You can choose Standard or Thorough, the latter of which you should choose if you have never run ScanDisk. Since it can take some time (up to a couple of hours), choose your time appropriately. If you need your computer before the scan finishes, it is OK to stop it, and start it again at a later time. It will take less time, as some of the scan has been done. However, because of the requirement to go through Step 1 - deleting unwanted files - should be done before running ScanDisk, it is obviously better to complete it in one sitting if possible.
Step 3: Defrag
When you create, move, copy, update, rewrite and delete files from your computer, they get fragmented. The computer can keep track of these fragments belonging to a single file, but it will take longer to display. To optimise computer performance, periodic defragmentation, or the process of reorganizing the contents of a disk so that all of a file's contents are written in a single contiguous block, is desirable. To run a defrag, which should be done immediately after running ScanDisk,
Go to Start>Programs>Accessories>System Tools>Defrag ------------------
and see

Hope this helps you. :)

Let me start by saying this question comes up so often that I wrote this and saved it in a file to copy from, it's of course only my opinion. Right though.
1st there is a lot of discussion about whether you need to defrag in safe mode or in standard Windows. You do not need to go to safe mode in 98% of all instances if you use the commonly called or named; ME_defrag.
2nd there is also a lot of discussion about shutting down everything running except explorer and systray. You do not need to do this in 98% of all instances if you use Me_defrag.
You can get this version of defrag at one of the following sites: (bunch of pop-ups here)

There are many more sites that you can get ME_defrag but these will do.
Once you have it (there is a self installing version and a manual install version) all you have to do is make sure the file is renamed to defrag.exe and move it into the C:\Windows directory. You will get a prompt asking if you want to replace the original defrag.exe, just say YES.
This is a small file. Only 209 kb.
Occassionally one of the sites will name it ME_Defrag.exe. That's why I mentioned to rename it.
There is also controversy about whether this was created by Micosoft as part of Win95 or ME. In my opinion, neither. It was part of the original NT OS disk keeper. I do know this, I've used it on Win95a, Win95B, Win98FE and Win98SE and never had a problem. I've run it without shutting any open apps including anti-virus and it always finishes. The only exception to this was a laptop with IBM Client Access installed and running a connection to an AS-400.
The first noticable difference in this version is that it gives you options. The default will move all your apps to the front for faster loading and I found this to work with a machine that had dozens and dozens of apps. To do this the first time takes a little while but succeeding runs are very fast. I recommend not using that option on the first run if you can't complete a defrag or have never defragged just to save time.
I've had people reply back on this board that using this version got them from 45 minutes on 30 and 40 GB drives to 3 to 5 minutes.
Also, if you are concerned, I recommend a once-a-week defrag. Others disagree but if you use your PC for more than just a mail box then it can only help. It can't hurt.
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