A method for inspection includes irradiating, with a focused beam, a feature formed on a semiconductor wafer, the feature including a volume containing a first material and a cap made of a second material, different from the first material, that is formed over the volume. One or more detectors positioned at different angles relative to the feature are used to detect X-ray fluorescent photons that are emitted by the first material in response to the irradiating beam and pass through the cap before striking the detectors. Signals output by the one or more detectors at the different angles in response to the detected photons are processed in order to assess a quality of the cap.