Abstract: A method, a non-transitory computer readable medium and a system for focusing an electron beam. The method may include focusing the electron beam on at least one evaluated area of a wafer, based on a height parameter of each one of the at least one evaluated area. The wafer includes a transparent substrate. The height parameter of each one of the at least one evaluated area is determined based on detection signals generated as a result of an illumination of one or more height-measured areas of the wafer with a beam of photons. The illumination occurs while one or more supported areas of the wafer contact one or more supporting elements of a chuck, and while each one of the one or more height-measured areas are spaced apart from the chuck by a distance that exceeds a depth of field of the optics related to the beam of photons.