That's strange. I've cleaned off fingerprint marks from my B+W MRC filters with microfiber cloth before and it was a 3 wipe process at most. The cloth you used might have been somewhat dodgy?
Anyway, try eclipse solution (available from cathay) and lens tissue (available almost everywhere i think). Canon is using the same stuff (amongst other mysterious liquids) to clean lenses in their service area. How do I know? Because a technician forgot to delete a test picture they took while checking my camera.