Light reflected by a sample surface region and a reference surface interfere. A detector senses light intensity at intervals during relative movement along a scan path between the sample surface and the reference surface to provide a series of intensity values representing interference fringes. A data processor receives first intensity data including a first series of intensity values resulting from a measurement operation on a surface area of a substrate and second intensity data including a second series of intensity values resulting from a measurement operation on a surface area of a thin film structure. A gain is determined for each thin film of the thin film structure. Substrate and apparent thin film structure surface characteristics are determined on the basis of the first and second intensity data, respectively. The apparent thin film structure surface characteristic is modified using the substrate surface characteristic and the determined gain or gains.