Just take enough off to clean them up. .002"-.003" should do it. You want to make sure that your head gasket seals properly.
If you want to, you can very carefully remove some of the material from the combustion chamber with a dremel or similar too. If you look at the 3l heads and the 2.5 heads side by side, you'll notice that there is 2 "bumps" between the valves. I would recomend taking material from there. It will lower compression and recude the possibility of detonation.