System and method for EMI shielding for a CD-SEM are described. One embodiment is a scanning electron microscope (“SEM”) comprising an electron gun for producing an electron beam directed toward a sample; a secondary electron (“SE”) detector for detecting secondary electrons reflected from the sample in response to the electron beam; and a dual-layer shield disposed around and enclosing the SE detector. The shield comprises a magnetic shielding lamina layer and a metallic foil layer.