A substrate is irradiated by primary electrons and secondary electrons generated from the substrate are detected by a detector. A reference die is placed on the stage to obtain a pattern matching template image including feature coordinates of the reference die. A pattern matching is performed with an arbitrary die in a row or column including the reference die using the template image to obtain feature coordinates of the arbitrary die. An angle of misalignment is calculated between the direction of the row or column including the reference die and one of the directions of movement of the substrate on the basis of the feature coordinates of the arbitrary die and those of the reference die. The stage is rotated to correct the angle of misalignment to conform the direction of the row or column including the reference die with the one of the directions of movement of the substrate.