The basic unit of a modern electron microscope incorporates a computer, a ROM, and a RAM. According to this invention, an external computer connected with the microscope also has a RAM. In the initial condition, the contents of the ROM in the microscope are read into the RAM of the external computer. When the magnification is set to a desired value, the external computer selects currents which are fed to the electron lenses and deflector coils, corresponding to the two values of magnification closest to the desired value of magnification, from the data stored in the ROM. Then, the computer calculates the currents which should be fed to the lenses and coils, corresponding to the desired value of magnification, from the selected values. The obtained data is held in either RAM. The external computer controls the lenses and coils according to the data held in this RAM.