I want to drill very precise multiple holes (0.5 - 1mm diameter) on a sheet of substrate (similar to PCB but softer) reproducibly using a cheap chinese CNC mill. The sheet is already marked with circles where the holes should be made. I am aware that the XY 00 can be set every time i place a substrate workpiece on the bed. However, the substrate overall dimensions are not always accurate and therefore, there will always be some rotational misalignment of the entire layout around the z axis each time i place a new substrate.

I am wondering if there is any way of manually providing the software 2 or more reference points across the substrate (e.g. one at xy=00 and others at the far end of the substrate) so it knows the angle of rotation and maintain the alignment and hole locations precisely within circles on the substrate matched with the CAD drawing?