A calibration leveling system and method are provided which improve printing and imaging at the nanoscale including improved tip-based deposition and nanolithography. The system can include a scanning probe instrument having a video camera with an adjustable lens. The scanner can be coupled to a one or two dimensional array of cantilevers comprising cantilever tips for imaging or printing. The scanning probe instrument has one or more motors for controlling the scanner in the z-axis. The z-axis motors position the scanner so that the cantilever tips are in a level orientation relative to the surface of a substrate. Once the cantilever tips are level with the substrate, the positions of the z-axis motors can be recorded for future reference.