I recently decided to re-align my screen protector and I ended up using a razor blade from a safety razor. Works great, just align the blade along an edge and gently nudge an end under one of the protector's corners and lift it enough to be able to grab it and do the rest with your finger. Worked great for me and left no marks at all.

Another method would be to stick a piece of tape or sticky tac to one of the corners and then lift it off, this method will probably leave some residue on the protector though.