Can you post pics? I have only ever pulled a couple of sports autos with major fingerprints, but I think they give the card some character, it makes me think they were chowing down some PO-TA-TOE (as Samwise the great would say) chips when they were signing.
Although I have no idea how to get them off, and be careful, it is probably better to have fingerprints than a damaged card without

Although I am cracking up just thinking of you sitting there with you cotton gloves trying to rub them off

It is just to funny.