The invention relates to a method for operating a measurement system containing a scanning probe microscope, in particular an atomic force microscope, and to a measurement system for examining a measurement sample using a scanning probe microscope and for optically examining said sample. In the method, an optical image of a measurement section of a measurement sample to be examined, said image being recorded with the aid of an optical recording device, is displayed on a display apparatus, a choice of a position in the optical image is detected, and, for a scanning probe measurement, a measurement probe which is configured for the scanning probe measurement is moved, using a movement apparatus which moves the measurement probe and the measurement sample relative to one another, to a measurement position, which is assigned to the selected position in the optical image in accordance with coordinate transformation, by virtue of the movement apparatus being controlled in accordance with the coordinate transformation, wherein a previously determined assignment between a coordinate system of the optical image and a coordinate system of a space covered by movement positions of the measurement probe and the measurement sample is formed with the coordinate transformation, wherein the movement positions comprise the measurement position.