This not only helps you run Scandisk/Defrag in normal mode easier but it also helps to clean up the excess garbage floating around that these programs don't need to scan or defrag anyhow. You can skip all of this if you want to and just run your scandisk and defrag from safemode if that's all you want.
These may seem long and complicated, but quite a few of these things won't pertain to your personal system and installations...you'll know which ones you don't have to do.
First make sure that you have emptied all TEMP folders (C:\TEMP C:\TMP and C:\Windows\TEMP) You probably don't have the first two so if you don't, it's ok.
Second, open Scandisk and click Advanced and put check marks in the following:
Notify you only if errors are found
Delete Cross-Linked Files
Free File Fragments
Check for Invalid Names,Dates,Times
Check Host first
Put a check in AutoFix Errors (most errors will come from the Temp.Int.Files folder so by checking this, you won't be notified of any errors individually that it finds, but if you clear that cache ahead of time in IE/Properties\Delete files on the Temp.Int.Files area, you can leave this box unchecked so that any other errors it finds will open a window giving you options of what to do with the errors..such as Repair,Delete, or Ignore and Ignore is about the stupidest one I've seen)
Empty the Recycle Bin...no need to Scandisk and Defrag this, especially if it has lots of files in it still that you have removed and forgotten about.
If you have MSOffice or any of its programs installed, you should (my opinion) also stop FindFast from running completely. It 'hits' your harddrive every couple of minutes searching all drives and partitions uselessly so that it can be 'ready' just in case you decide to open an Office program. This interferes badly with your system speed and also with Scandisk and Defrag. I don't know anybody who keeps this program around for long once they realize how useless it is. Go to Start\Programs\Startup and delete the icons (black) that are there for FindFast. Now go to Control Panel\FindFast and open it up and click Edit, click Delete Indexing for each drive and partition listed in the white box below it. That will stop the entire program from running.
Now close all running programs using CTRL-ALT and the DEL key (press the DEL key only once to get the menu) except Explorer and Systray. (There is a free program at http://www.pcmag.com/article/0,2997,s%253D1478%2526a%253D10165,00.asp called EndItAll that will do this for you and is highly recommended...the pcmag link is to version 2 and is more complicated to configure for a newbie than Version 1 listed below)
EnditAll Version 1
And also choose NONE for a screensaver until Scandisk and Defrag have been run successfully.
Now run the program...If you have had many File000.chk files building up in the C: root it will remove them giving you much harddrive space that was being used up with those files.
Once Scandisk has been run and is error free, open Defrag and click Settings. Take the check mark out of "re-arrange my files" and make sure there is a check mark in "every time I run this program". This will stop Defrag from putting all of the MS programs at the front of the defragged harddrive...which takes alot of time to run if you have many MS programs installed on your system. The program actually gets faster as it does this because it is remembering where the files were when it last ran, but it takes at least 20 times of running Defrag before you would notice any difference in the speed, so it could conceivably take all day and night to defrag a very large harddrive that isn't partitioned, so most people turn off this 'feature'.
Now run Defrag.
If this doesn't work for you and you still can't scandisk or defrag in normal windows mode, reboot the computer, press F8 a couple of times after the first bootscreen leaves, and choose Safemode from the menu. Now run scandisk and defrag from safemode instead.
I can't do a Scan disk(error mess-tries 10 X's then stops,retries then stops)what's-up.