A method for calibrating a CNC machine including providing instructions for machining a surface of a distortion-free object, selecting a true axis of movement of a toolhead of the machine using the instructions, instructing the toolhead to travel on an object to be machined along the true axis of movement, but where the toolhead actually travels along an actual axis that is deviated from the true axis as a result of the surface distortions on the object to be machined, selecting multiple points along the actual axis traveled by the toolhead on the object to be machined, comparing the distance of the multiple points along the actual axis from the true axis to determine offset amounts from the true axis corresponding to a lack of straightness of the object to be machined, and modifying the instructions to compensate for the offset amounts before uploading the instructions to a CNC controller.