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
Replace Log
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.
TONI
Any help with defraging, goes until it needs to do the files most used and will only get to about 3%. Got ME version loaded, havent had problems before with this.
Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic