An interferometer system (2) directs light along a sample path (SP) towards a sample surface (7) and along a reference path (RP) towards a reference surface (6). Light reflected by a sample surface region and by the reference surface interfere. Sensing elements (SE) sense interference fringes at intervals along a scan path to provide a set of intensity data. A coherence peak position determiner (201) determines from the intensity data set a position on the scan path that corresponds to the height of the surface region. An amplitude determiner (202) determines amplitude data representing the amplitude of the intensity data at the determined height position. A modified surface height calculator (207) calculates modified height data by modifying the height data by a correction factor determined using the corresponding amplitude data and a correction parameter provided by a correction parameter provider (260).