It is to provide a technology that can quickly process many measurement points on a substrate by a primary charged particle beam. In a control system, with respect to each measurement point (irradiation position of the primary charged particle beam) on a wafer, a calculator obtains a probability of a surface potential at a relevant measurement point that is obtained from a surface potential distribution function of the wafer and is stored in a data storage unit. Based on the probability, the calculator determines an amplitude of a set parameter (for example, retarding voltage) of charged particle optics at the relevant measurement point. Then the calculator checks the focus state of the primary charged particle beam by changing the set parameter in the range of the determined amplitude, and determines the set parameter to be used for measurement.