A scanning probe microscope, such as an atomic force microscope, include a z-stage and a bridge structure comprised substantially free of Invar. A scanner containing a probe is mounted to the z-stage, which is movable in the z-axis to raise and lower the probe. A drift compensation system is provided to reduce thermal drift of the z-stage and the bridge. The drift compensation system includes heating elements thermally coupled to the z-stage and the bridge, ambient temperature sensors, and a controller to actively control the heating elements to maintain the bridge and the z-stage at an elevated temperature.