Methods, systems, and apparatus, including medium-encoded computer program products, for automatic generation of probe path for surface inspection and part alignment. A mesh model is obtained of at least a portion of a three dimensional model of a part to be manufactured using a computer-controlled manufacturing system. Vertex points from the mesh model are collected to be an initial set of probing points in a three dimensional space of a working coordinate system of the computer-controlled manufacturing system, and filtering out points are filtered out from the initial set of probing points based on coverage of the least a portion of the three dimensional model to produce a final set of probing points. The final set of probing points is provided for use in alignment or surface inspection of the part by the computer-controlled manufacturing system.