Abstract: A scanning probe microscope and method for operating the same to correct for errors introduced by a repetitive scanning motion are disclosed. The microscope includes an actuator that moves the probe tip relative to the sample in three directions. The actuator executes a repetitive motion, characterized by a repetitive motion frequency, in one of the directions, and changes a distance between the sample and the probe tip in a second one of the directions. A probe position signal generator generates a probe position signal indicative of a position of the probe tip relative to the cantilever arm. A probe signal correction generator generates a corrected probe position signal by correcting the probe position signal for errors introduced by the repetitive motion. A controller maintains the probe tip in a fixed relationship with respect to the sample in the second one of the dimensions based on the corrected probe position signal.