A method for inspection includes irradiating a sample using an X-ray beam, which is focused so as to define a spot on a surface of the sample. At least one of the sample and the X-ray beam is shifted so as to scan the spot along a scan path that crosses a feature on the surface. Respective intensities of X-ray fluorescence emitted from the sample responsively to the X-ray beam are measured at a plurality of locations along the scan path, at which the spot has different, respective degrees of overlap with the feature. The intensities measured at the plurality of the locations are processed in order to compute an adjusted value of the emitted X-ray fluorescence over the scan path. A thickness of the feature is estimated based on the adjusted value.