Embodiments of systems and methods for measuring a surface topography of a semiconductor chip are disclosed. In an example, a method for measuring a surface topography of a semiconductor chip is disclosed. A plurality of interference signals each corresponding to a respective one of a plurality of positions on a surface of the semiconductor chip are received by at least one processor. The plurality of interference signals are transformed by the at least one processor into a plurality of spectrum signals each corresponding to the respective one of the positions on the surface of the semiconductor chip. The spectrum signals are classified by the at least one processor into a plurality of categories using a model. Each of the categories corresponds to a region having a same material on the surface of the semiconductor chip. A surface height offset between a surface baseline and at least one of the categories is determined by the at least one processor based, at least in part, on a calibration signal associated with the region corresponding to the at least one of the categories. The surface topography of the semiconductor chip is characterized by the at least one processor based, at least in part, on the surface height offset and the interference signals.