why don't you try to use effective antivirus software (avira, avast, kaspersky.....) to remove it? free or trial versions of it...just make sure you update their virus signatures/definitions..

hmm....basically most of the viruses in flash drives wouldn't affect the current files in the drive. they copy another malicious file to the flash drive. i hope those are the viruses which are infected.

oh...never mind...hmm....you mean actually in the drive there's a virus affecting one or several files for example? and you don't want to delete them?

actually it's possible for antiviruses to clean the virus from the file(s), but with a low chance for the file to be recovered. cause most antiviruses put delete as the main or the only possible action in order to remove the virus from the flash drive.