Where should the center of the spindle be if I want to mill the side of a part?

To calculate where the center of the spindle should be, take the radius of the end mill you are using, and subtract how much material you would like to cut off per pass. The center should be this far away from the edge. For example, if you are cutting 0.125” in a single pass, and the radius of your end mill is 0.50”, the center of the spindle should be 0.375” away from the edge.