Usually .doc files are "safe" from malware, which prefers to hide itself elsewhere on your hard drive. You do not need to move them to your desktop, although it would be a smart plan to archive them to disk since they are important. You can---and should---scan them when you copy them back to your hard drive.
If you deleted files as a result of your scanning, this could easily have changed the contents of your HJT log. Please run a new log and append it to the original so the team member reviewing your log is not looking at bad data (along with a note about what you ran).
Edited by jgweed, 14 April 2008 - 02:07 PM.