A dual stage scanning instrument includes a sensor (60) for sensing a parameter of a sample (90) and coarse and fine stages (80,70) for causing relative motion between the sensor (60) and the sample (90). The coarse stage (80) has a resolution of about 1 micrometer and the fine stage (70) has a resolution of 1 nanometer or better. The sensor (60) is used to sense the parameter when both stages cause relative motion between the sensor assembly (60) and the sample (90). The sensor (60) 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 a long scan at a coarser resolution and short scans at high resolution using the same probe tips at fixed relative positions, data obtained from the long and short scans can be correlated accurately.