The present invention relates to a method for mutually aligning a scanning electron microscope SEM and a light microscope LM by creating a change (61) in the detected light signal of the light microscope LM by illuminating a substrate with an electron beam, correlating the position of the electron beam in the coordinate system of the scanning electron microscope SEM to the position of the observed change in the detected light signal in the coordinate system of the light microscope LM, and relatively shifting the scanning electron microscope SEM and the light microscope LM with respect to one another to a desired relative position of the coordinate systems (60, 62).