A surface topography of a sample with a transparent surface layer is measured using surface topographies of a reference sample. The surface topographies of the reference sample are measured before and after the deposition of an opaque film over the surface layer. A surface topography of the sample is measured at the same relative positions as the surface topography measurements of the reference sample. A height difference at multiple corresponding positions on the sample and the pre-opaque film reference sample is determined. The actual surface height of the reference sample at each position is known from the surface topography of the post-opaque reference sample. The actual surface topography of the sample is determined by combining the actual surface heights of the reference sample with the determined height differences. The resulting surface topography of the sample may be used to characterize the sample, such as detecting defects on the sample.