Go slow, only do 1 or 2 nails per day if he's really being difficult.
You can also try the bath. I've used it when a hedgehog is being difficult and I wanna get the clipping done and over with. Just remember that the warm water will make toes bleed faster if you clip the quick. It isn't a huge deal, just don't let it scare you.
Hedgehog Forums 
