A method for inspection of a sample includes directing an excitation beam to impinge on an area of a planar sample that includes a feature having sidewalls perpendicular to a plane of the sample, the sidewalls having a thin film thereon. An intensity of X-ray fluorescence (XRF) emitted from the sample responsively to the excitation beam is measured, and a thickness of the thin film on the sidewalls is assessed based on the intensity. In another method, the width of recesses in a surface layer of a sample and the thickness of a material deposited in the recesses after polishing are assessed using XRF.