What prevents you from formatting it?
Open Windows Explorer or My Computer and navigate to your pendrive. To open Windows Explorer, Hold the [Windows Key] + [E]. Once you find your pendrive, right click it and select "Format" and follow the directions given. Do you receive error messages? You shouldn't. I can't imagine why you would. But if you do, post them and I'll try to help you further.
How did you get a virus on your pendrive? It shouldn't automatically run anyway unless you set it up to. Is there a file called "autorun.inf" on your pendrive? Simply delete it and the virus won't automatically execute when you insert it. Again, I'm not sure how this can happen, but anything's possible. Are you SURE that there's a virus on the drive? Positive?
Ryeguy
January 2009