1. A control system 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, wherein the control system is arranged to set up an array of pixels, each pixel having an area that maps to a finite spatial area of the sample surface and, for each measurement position, a spatial location of that position is determined empirically and the value of a data point measured is associated with the pixel whose mapping is to the sample area that includes the empirically-determined spatial location and wherein the data values associated with a single pixel area are combined to determine a final data value for that pixel position.