A control system 32, 75 is for use with a scanning probe microscope of a type in which measurement data is collected at positions within a scan pattern described as a probe and sample are moved relative to each other. The control system is used in conjunction with a position detection system 34 that measures the position of at least one of the probe and sample such that their relative spatial location (x, y) is determined. Measurement data may then be correlated with empirically-determined spatial locations in constructing an image. The use of empirical location data means that image quality is not limited by the ability of a microscope scanning system to control mechanically the relative location of probe and sample.