A measurement system comprising: a radiation source arranged to generated a detection beam; a probe; and a probe positioning system arranged to move the probe from an un-aligned position in which it is not illuminated by the detection beam, to an aligned position in which it is illuminated by the detection beam and the detection beam is reflected by the probe to generate a reflected detection beam. A scanner generates a relative scanning motion between the probe and a sample, the sample being aligned with the probe and interacting with the probe during the relative scanning motion. A sensor detects the reflected detection beam during the relative scanning motion to collect a first data set from the sample. A second device is provided for modifying the sample or obtaining a second data set from the sample. A sample stage is arranged to move the sample in accordance with an offset vector stored in a memory so that it becomes un-aligned from the probe and aligned with the second device.