A method for calibrating a scanning charged particle microscope, such as a scanning electron microscope (SEM), is provided. The method includes dividing a wafer into a plurality of regions; preparing, on each of the plurality of regions, a pattern including a first periodic structure interleaved with a second periodic structure, the first and second periodic structures having an induced offset; determining an actual pitch the first and second periodic structures and thereby determining actual induced offset on each of the plurality of regions; selecting a plurality of regions from among the plurality of regions; measuring, by the SEM, a pitch of first and second periodic structures on each of the plurality of regions; and performing linearity calibration on the SEM based on the determining and the measuring.