There are a couple programs people use, if you google pcb milling or diy pcb milling they come up.
Most of them are eagle plugins:
http://www.embeddedtronics.com/pcb.htmlThere are also a lot of tips on keeping the board flat and what cutters to use. If you are only taking one or two thou off the top of the board it can be challenging to hold it down so that the surface is perfectly level.