A method for calibrating a computer numerical control (CNC) machine for milling an implant abutment includes creating a calibration part by milling reference surfaces with predetermined coordinates into a blank stock held by a CNC fixture. By measuring the milled reference surfaces of the calibration part and comparing the measurements to the predetermined coordinates, the CNC fixture can be accurately placed in a global coordinate system, thereby allowing for the derivation of shifts in an abutment geometry in each of the x, y, and z axes in order to align a fabricated abutment relative to the CNC fixture. The shifts may then be used to adjust a control of the CNC machine to match a present state of the CNC machine and the CNC fixture.
