An electron microscope equipped with a scanning tunneling microscope. The electron microscope comprises a holder, a scanning tunneling microscope scanner having a tip, and a shift mechanism. A sample is fixed inside the holder that is mounted between the upper pole piece and the lower pole piece of an objective lens. The shift mechanism moves the scanner in two directions parallel to the surface of the sample and in a direction vertical to the sample surface. The tip is poised above a desired portion of the sample by driving the shift mechanism while observing the tip and either a reflection electron microscope image or a transmission electron microscope image of the sample. Then, the scanner uses the tip to scan the sample surface to obtain a scanning tunneling microscope image.