Improvements for rapidly calibrating and automatically operating a scanning probe microscope are disclosed. A central component of the SPM is the force transducer, typically a consumable cantilever element. By automatically calibrating transducer characteristics along with other instrumental parameters, scanning parameters can be rapidly and easily optimized, resulting in high-throughput, repeatable and accurate measurements. In contrast to dynamic optimization schemes, this can be accomplished before the surface is contacted, avoiding tip or sample damage from the beginning of the measurement process.