A method for specifying design rules for a manufacturing process includes providing a training set of 3D point meshes that represent an anatomical structure, for each 3D point mesh, finding groupings of points that define clusters for each shape class of the anatomical structure, calculating a prototype for each shape class cluster, and associating one or more manufacturing design rules with each shape class prototype. The method includes providing a new 3D point mesh that represents an anatomical structure, calculating a correspondence function that maps the new 3D point mesh to a candidate shape class prototype by minimizing a cost function, calculating a transformation that aligns points in the new 3D point mesh with points in the candidate shape class prototype, and using the rules associated with the shape class prototype, if the candidate shape class prototype is successfully aligned with the new 3D point mesh.