I assume that you want to determine the workpiece zero points. There are basically 2 ways to do this:

-Scratching the workpiece zero points with the clamped milling cutter.
-spotting the workpiece zero points with an edge finder, e.g. Proxxon 2-piece edge finder set

By the way, these ways do not differ for "big" production machines. The 3D probe has a ball as a scanning device and is otherwise comparable with an edge finder. :)