You'll want to use Mach 3 software for your CNC control. There's a group on CNCZone for this and another good one on Yahoo. Start reading.
Circuit board software outputs files as gerber design for the traces. I found a freeware program on the web to convert this to a .dxf file. Then used a CAM (Mastercam in my case) program to write the G code program for the CNC control.
The drill holes are output as excellon type files. These can be quickly manually edited into a CNC Gcode program.
I did this once for experience, then found out you can just send your design out and have four copies of your board made for $50.
Karl


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