An electron microscope comprising: an electron beam source; electron lenses (12,14,16) disposed in an electron optical column; a cooling section disposed in the electron optical column and operative to cool an adsorptive member to thereby adsorb contaminant materials that contaminate a sample; a heating section for heating the adsorptive member; a detector disposed in a detection chamber and operative to detect an electron beam transmitted through the sample; a first vacuum pumping unit connected into the electron optical column via a first vacuum gate valve; a second vacuum pumping unit connected into the detection chamber and also connected into the electron optical column via a second vacuum gate valve, the second vacuum pumping unit being capable of operating at pressures higher than pressures at which the first vacuum pumping unit can operate; and a controller arranged to perform an operation to switch the mode of operation of the electron microscope from a first mode where the electron lenses are excited and the second vacuum pumping unit is on to a second mode where the electron lenses are not excited and the second vacuum pumping unit is off; wherein, during said operation to switch the mode of operation from the first mode to the second mode, the controller is arranged to perform the steps of: closing the first vacuum gate valve, opening the second vacuum gate valve, turning the first vacuum pumping unit off, and vacuum pumping the interior of the electron optical column by the second vacuum pumping unit; then controlling the heating section to heat the adsorptive member whilst the first vacuum gate valve is closed and the first vacuum pumping unit is turned off; then turning the first vacuum pumping unit on, opening the first vacuum gate valve, closing the second vacuum gate valve, and vacuum pumping the interior of the electron optical column by the first vacuum pumping unit; turning off the second vacuum pumping unit; and turning off the electron lenses. an electron beam source; electron lenses (12,14,16) disposed in an electron optical column; a cooling section disposed in the electron optical column and operative to cool an adsorptive member to thereby adsorb contaminant materials that contaminate a sample; a heating section for heating the adsorptive member; a detector disposed in a detection chamber and operative to detect an electron beam transmitted through the sample; a first vacuum pumping unit connected into the electron optical column via a first vacuum gate valve; a second vacuum pumping unit connected into the detection chamber and also connected into the electron optical column via a second vacuum gate valve, the second vacuum pumping unit being capable of operating at pressures higher than pressures at which the first vacuum pumping unit can operate; and a controller arranged to perform an operation to switch the mode of operation of the electron microscope from a first mode where the electron lenses are excited and the second vacuum pumping unit is on to a second mode where the electron lenses are not excited and the second vacuum pumping unit is off; wherein, during said operation to switch the mode of operation from the first mode to the second mode, the controller is arranged to perform the steps of: closing the first vacuum gate valve, opening the second vacuum gate valve, turning the first vacuum pumping unit off, and vacuum pumping the interior of the electron optical column by the second vacuum pumping unit; then controlling the heating section to heat the adsorptive member whilst the first vacuum gate valve is closed and the first vacuum pumping unit is turned off; then turning the first vacuum pumping unit on, opening the first vacuum gate valve, closing the second vacuum gate valve, and vacuum pumping the interior of the electron optical column by the first vacuum pumping unit; turning off the second vacuum pumping unit; and turning off the electron lenses. closing the first vacuum gate valve, opening the second vacuum gate valve, turning the first vacuum pumping unit off, and vacuum pumping the interior of the electron optical column by the second vacuum pumping unit; then controlling the heating section to heat the adsorptive member whilst the first vacuum gate valve is closed and the first vacuum pumping unit is turned off; then turning the first vacuum pumping unit on, opening the first vacuum gate valve, closing the second vacuum gate valve, and vacuum pumping the interior of the electron optical column by the first vacuum pumping unit; turning off the second vacuum pumping unit; and turning off the electron lenses.