You can re-stamp, (not engrave!), the serial number as chuck stated, but it MUST be in a different place. Even if you can't see the original, it can be brought back up using certain chemicals and techniques. I've done it many times. (re-stamp during re-finishing, not bring up old numbers)
Once, when an old pistol with no number was present, I contacted the local ATF office for guidance. Their reply was "just put a number on it." "what number" I asked? "It doesn't matter, as long as it has a number." It was not a stolen gun like the one VI shooter showed.
I have also refused to work on firearms where the serial number was purposely defaced in an attempt to decieve or mis-lead.THAT is definitely a no-no with ATF.
FWIW,
Emri