A probe alignment tool (10) for scanning probe microscopes utilizes an attached relay optics to view the scanning probe microscope probe tip (40) and align its image in the center of the field of view of an optical microscope (36). Adjustments to optical microscope motorized stages (50) and (60) along with adjustments of scanning probe microscope stages (44), (46) and (58) allow determination of a path and distance from the center of the field of view to the probe tip (40). From such determination a target area to be examined by the scanning probe microscope may be positioned precisely and accurately under the probe tip (40). Replacement of a scanning probe microscope probe tip (40) in an atomic force microscope unit (42) may be accomplished without the loss of alignment measurements.