@Odhiambo & Mr. Lawi
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The way I do it? Simply get Hiren's Ultimate Boot CD (UBCD), boot off it, and you have a Windows running off a memory disk which won't get infected anyway. Open the flash disk, goto Tools->Folder Options->View, show hidden files and folders->Ok.
You have all the files showing right on your face. Select all, deselect the ones you don't want to delete (eg the Firefox Setup 3.0.11.exe, etc) and shift+delete the files/folders. Delete autorun.inf and any other funny named command files the virus had created and voila! Reboot/Eject UBCD and ask for the next virus victimé:-)
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Being a lazy chap, I achieve the same by using nero. I came to discover that some applications are actually made to "see" *.
I simply go through the steps of making a new compilation, select the pesky files and kick them from within nero.