A method for measuring damage (D) of a substrate (1) caused by an electron beam (2). The method comprises using an atomic force microscope (AFM) to provide a measurement (S2) of mechanical and/or chemical material properties (P2) of the substrate (1) at an exposure area (1a) of the electron beam (2). The method further comprises calculating a damage parameter (Sd) indicative for the damage (D) based on the measurement (S2) of the material properties (P2) at the exposure area (1a).