A system for controlling a tool-to-tool disparity between a plurality of scanning electron microscopes includes a measuring unit for measuring a tool-to-tool disparity between plural scanning electron microscopes based on information extracted from secondary electron images which are captured by imaging a reference pattern formed on a wafer, a tool state monitoring unit for monitoring tool states of each of the plural scanning electron microscopes, and an output unit for displaying on a screen a relationship between the tool-to-tool disparity between the plural scanning electron microscopes and tool states of each of the plural scanning electron microscopes monitored by the tool state monitoring unit. The tool state monitoring unit monitors the tool states of each of the plural scanning electron microscopes while imaging the reference pattern formed on the wafer by using each of the plural scanning electron microscopes.