Auto leveling is key to precise PCB milling. I wrote some open-source software that makes it possible to do auto-leveling on a CNC USB Controller-based machine like my chinese 3020 CNC. This software controls the actual control software so that it starts probing a circuit board in a grid-like manner, after which it can compensate for any misalignment and curvature in the GCode.
Discusses the limitations of my 3020 CNC machine as well as some of the ways to work around them, allowing me to successfully mill things like LEGO-compatible bricks and circuit boards.