I use the Great Planes "Slot Machine" which is an electric powered tool with two toothed blades that slide back and forth. It comes with blade sets that are made to match the different thickness nylon hinges like you are using. I usually don't use the CA hinges that come with some kits and ARFs and you can use this tool to open up existing sliced CA hinge slots or make new ones.

Ref. http://www.greatplanes.com/accys/gpmr4010.html

Jaybird