A method for programming a three-dimensional (3D) workpiece scan path for a metrology system comprising a 3D motion control system, a first type of Z-height sensing system, and a second type of Z-height sensing system that provides less precise surface Z-height measurements over a broader Z-height measuring range. The method comprises: placing a representative workpiece on a stage of the metrology system, defining at least a first workpiece scan path segment for the representative workpiece, determining preliminary actual surface Z-height measurements along the first workpiece scan path segment, and determining a precise 3D scan path for moving the first type of Z-height sensing system to perform precise surface Z-height measurements. The precise 3D scan path is based on the determined preliminary actual surface Z-height measurements. The precise 3D scan path may be used for performing precise surface Z-height measurements or stored to be used in an inspection program.