Calibration of scanning probe microscopes (SPM) for atomic (molecular) resolution scans can be carried out on crystalline surfaces. However, SPM scans with atomic resolution are often affected by drift and hence would give false calibration factors. We propose a method which allows to calibrate the SPM instrument eliminating the effects of drift in a first‐order approximation. Scans of the same surface are taken at different speeds and a linear regression is applied to the calibration factors calculated for each scan speed. Applying this method we succeeded in calibrating a commercial SPM system for atomic resolution scans with a precision of better than 2%. ©1995 American Institute of Physics.