Lithographic apparatus, system, method, computer program, and apparatus for height map analysis

A lithographic projection apparatus and method of manufacturing devices using such an apparatus is presented. The apparatus includes a level sensor to measure the height of a wafer in a plurality of points. The height info is sent to a processor which is arranged to create a measured height map using input from the level sensor. In one embodiment of the invention, the processor is also arranged to calculate an average die topology using the measured height map in order to produce a raw height map of the surface of the substrate, and to detect any focus spots on said surface of said substrate using the raw height map. By subtracting the average die topology, focus spots can be located more accurately than before.