Abstract: The invention provides a system and method for automatically, accurately, and repeatable aligning computer numerically controlled (CNC) movable machine components with respect to their respective degrees of freedom of motion. One embodiment of the invention, particularly useful for maintenance purposes, provides a programmable CNC programmer that uses a spindle mounted probe to measure at least two different positions of a point on a movable machine component to evaluate the geometric condition of the component with respect to a degree of freedom of motion of the component and issue alignment instructions to the machine operator. One embodiment provides the invention in a CNC computer program on a programmable media having a programmed set of instructions. The preferred embodiment uses the controller control the CNC machine's operation and spindle movement, perform the machine components' maintenance evaluation, and issue instructions for aligning the components in a consistent manner.