Probably the best way is to Ghost the drive to a spare, then Ghost it back.

Hi JAD,

Here are a few tips to consider when running Scandisk and Defrag.
1. Restart to the Command Prompt and do a thorough Scandisk on the
  drive first and repair any errors.
  Restart the computer. Hold down the CTRL key while the system is
  booting. This will take you to the Boot Menu then select Command
  Prompt Only. Run Scandisk on the drive from there by typing SCANDISK
  then press enter and let it perform a surface scan.
2. Close all running programs using Close Programs (Ctrl + Alt + Del)
  except Explorer.
3. Turn off screen savers and any power management
4. Delete Temp files and Temporary Internet Files
5. Empty the Recycle Bin
6. Do a virus scan with up to date virus software
   Free offer: eTrust EZ Armor Security Suite from Computer Associates
   http://www.my-etrust.com/microsoft/index.cfm
7. Disable PC-Cillin if installed
8. Turn off and disconnect DSL/Cable Modem
9. Run Ad-aware to remove any possible spyware
http://www.lavasoftusa.com/

Note: Defragging in Safe Mode is another option.

For more information on the subject check the links below:

List of Articles About the Disk Defragmenter Tool:
http://support.microsoft.com/support/kb/articles/q286/2/63.asp