Ok PCB milled now how to drill the holes ?

[HankMcSpank]

How this normally works is you design the pcb in something like eagle...you then run an excellon job in Eagle & it produces a drd file for all the drill holes, you then use that (for example I use Cambam to pull in the Eagle gerber files for the milling aspect, but there's a user plugin that runs excellon files.....the result is a 'point' for the drill at all the correct coords)

I'm wondering why you'd be thinking you should be drilling by eye? (your copper stock was already being milled by you machine...just get it to do the drilling first...simples! As the saying goes...why have a dog & bark yourself)