A scanning probe microscope system. A sample stage is provided along with a microscope arranged to collect data with a probe carried by the microscope from a sample carried by the sample stage. A probe/sample exchange mechanism is arranged to exchange the probe carried by the microscope with a new probe, and is also arranged to exchange the sample carried by the sample stage with a new sample. The probe/sample exchange mechanism comprises a transport structure which can move relative to the microscope and the sample stage; a probe carrier carried by the transport structure and adapted to carry the probe or the new probe when the probe is exchanged with the new probe; a sample carrier carried by the transport structure, wherein the sample carrier is adapted differently from the probe carrier to carry the sample or the new sample when the sample is exchanged with the new sample; and a drive system arranged to move the transport structure relative to the microscope and the sample stage when the probe is exchanged with the new probe and the sample is exchanged with the new sample.