But what establishes the center of each bore?
You as the operator have to indicate each cylinders centerline yourself and also touch the tool off at some designated height you determine and then designate a work offset in the CNC control panel to represent each cylinder and also the tool height, so when you create the program the tool knows where to go and how far to travel up or down so it won't crash into the block. Its all part of the setup process you have to do each time you start a new part.
