There are a few things to keep in mind when milling/routing PCBs.
The first is your PCB must be mounted perfectly square to the spindle. Your mills table will probably be off 0.002" or so end to end so you'll need to use your mill to machine a surface plate to mount your PCB material to. This is essential as your only trying to take off the copper which is very thin.
Second trying to do mill the board in a raster pattern will not work well. What I use and suggest is using Eagle PCB layout software (
http://www.cadsoft.de/) and PCBGcode (pcbgcode.org) to convert the Eagle board file into Gcode for Mach. This combination works very well. I have some pictures here on the forum of PCBs I have created this way.
Third you need the correct bit geometry for isolation routing. What works best is a 60 degree 'V' bit with a flute design for this application. Something like this:
http://soigeneris.com/shop/Precise_Bits_86618.aspx . Look about 1/2 way down the page for the type of V-bit I'm speaking of. At the bottom of the page you'll see 'Starter' kits that I put together to help folks get the most of the bits they will need to start milling PCBs. (Yes, I'm biased that is my web page. There are lots of other places that make similar bits. But I know the URL to mine really well

).
Isolation routing does not try to remove all copper between traces. It just takes multiple (you can set how many) passes around each trace to isolate it electrically from the others. This works very well and produces very good results. If you need to/want to remove large areas of copper you can put this in the rub-out layer in Eagle and use a small end mill (far less precise) to do so.
Hope that helps...