Abstract: A CNC apparatus has a memory configured to compensate for offsets in a pivot point. The machine tool has a head, a pivot point, a spindle, a table, and at least four axes including an X-axis, a Y-axis, a Z-axis, and a C-axis. A method for calibrating the CNC apparatus for controlling the machine tool includes placing an artifact of known height on the table, placing a plug having a known diameter on the spindle and touching the plug to the artifact in a plurality of orientations of the plug and in a plurality of locations of the plug and the artifact to determine uncalibrated X and Y pivot point locations at a plurality of orientations of the spindle. The uncalibrated X and Y pivot point locations are used to determine and store values in the memory of the CNC apparatus to compensate for offsets in the pivot point.