I prefer to use Boot CD's that either create a Physical Environment similar to an OS but not installed on the HDD, just running straight from the RAM or just run the scan from the CD prior to booting into Windows. Make any sense? It's more efficient to scan the entire HDD because if you're booted into Windows, there are a lot of files currently being used by something else that you will not be able to scan (or at least modify) with antivirus software.