We have a Quick Circuit at work that does a good job. Only problem is that you can't put vias under parts since our vias are just eyelets smashed into the vias. Also, we have all the through hole connections on the back to ensure we can solder to the pins.

The software came with the milling machine, and it takes gerber files and isolates the traces with a specified gap. I believe the system was pretty expensive, about $15k.