A method and apparatus for assessing a height of a specimen includes an electron beam unit having an electron beam source, lenses, a table for setting a specimen and controllable in a height direction, and a detector, and a height detection system for detecting height of the specimen set on the table while the specimen is irradiated by an electron beam. The height detection system further includes an illumination system, a collection system, first and second detectors, a device configured to receive output signals from the first and second detectors while the specimen is irradiated by the electron beam and to generate a comparison signal from the output signals, wherein the comparison signal is responsive to the height of the specimen.