The virus/trojan is either loaded from your pen drive (if you're "lucky") or it has moved to your HDD and is accessing its parent on the pen drive.
Putting the pen drive into a another PC and doing nothing else than reformatting it should clear the pen drive. Or throw it away!
But you now need to look at your HDD and make sure that nothing has happened there. Fingers crossed and fear the worst.
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Posting Virtuoso
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since Aug 2007