recently i scanned my pendrive for viruses and trojans using mcafee.mcafee couldnt remove one file winnthb.exe which remained in pendrive. however i knew another method.
i started cmd.exe in vista home premium.
removed system and hidden properties of the files of the removable drive and then deleted the file. 
click on start ,then run—type cmd and press enter.you can see command prompt pop up.
f: (removable drive —->flash drive or pen drive)
f:>attrib -s -h -r (removes superhidden property so that it becomes a regular file)
f:> dir (to find list of files )
f>del filename.extension
that is all.file gets deleted.
i thought of building a windows application to eliminate the process of using the commands.but i am stuck at deleting few autorun.inf files. i am getting unauthorisedaccessexception error,have to figure out the way soon.
edit: got through the tough part ,want some deadly pen drive viruses now.
will continue….
update: my simple application is ready to download .please report any bugs if any.
