A method includes irradiating a surface of a sample, which is made-up of multiple types of materials, with a beam of primary electrons. Emitted electrons emitted from the irradiated sample are detected using multiple detectors that are positioned at respective different positions relative to the sample, so as to produce respective detector outputs. Calibration factors are computed to compensate for variations in emitted electron yield among the types of the materials, by identifying, for each material type, one or more horizontal regions on the surface that are made-up of the material type, and computing a calibration factor for the material type based on at least one of the detector outputs at the identified horizontal regions. The calibration factors are applied to the detector outputs. A three-dimensional topographical model of the surface is calculated based on the detector outputs to which the calibration factors are applied.