A method and system for adapting a CNC machine tool path from a nominal workpiece shape to an actual workpiece shape. The method includes defining a grid of feature points on a nominal workpiece shape, where the feature points encompass an area around the machine tool path but do not necessarily include points on the machine tool path. A probe is used to detect locations of the feature points on an actual workpiece. A space mapping function is computed as a transformation from the nominal feature points to the actual feature points, and the function is applied to the nominal tool path to compute a new tool path. The new tool path is used by the CNC machine to operate on the actual workpiece. The feature points are used to characterize the three dimensional shape of the working surface of the actual workpiece, not just a curve or outline.