A dual stage scanning instrument includes a sensor for sensing a parameter of a sample and coarse and fine stages for causing relative motion between the sensor and the sample. The coarse stage has a resolution of about 1 micrometer and the fine stage has a resolution of 1 nanometer or better. The sensor is used to sense the parameter when both stages cause relative motion between the sensor assembly and the sample, The sensor may be used to sense height variations of the sample surface as well as thermal variations electrostatic, magnetic, light reflectivity or light transmission parameters at the same time when height variation is sensed. By performing along scan at a coarser resolution and short scans a high resolution using the same probe tip or two probe tips at fixed relative positions, data obtained from the long and short scans can be correlated accurately.