A scanning probe microscope compensates for relative drift between its upper structure that includes a probe and a scanner that scans the probe in a straight line and a lower structure that includes a sample stage and a scanner that scans the sample stage in a plane. A light beam from the upper structure is initially aligned with a center of a position sensitive photo detector (PSPD) disposed on the lower structure at a predetermined position of the sample stage and any subsequent misalignments of the light beam with the center of the PSPD at the predetermined position of the sample stage are determined to be caused by drift and compensated by the scanning probe microscope.