My guess is you are talking about the lower row of head studs under the header flange. It will often interfere with the flanges at least on the outside corners of the headers, or maybe all across the bottom.

You have a couple choices:

1) Get the correct length ( shorter) studs from ARP

2) Remove existing studs and cut the tops down. ( usually helps to radius the top of the stud as well in a cicular type pattern)

3) Also get 12 point nuts which will sometimes help with a little extra clearance.

Good luck.