An improved method for rapidly and accurately modifying small structures, including structures on a micron or nanometer scale, suitable for the repair of defects in lithographic photo-masks and semiconductors on a nano-scopic level. Features or samples repaired may be conductive or non-conductive. A single instrument can be employed to both observe the surface of the mask or wafer, and to effectuate the repair of conductive and non-conductive features thereon. Using a Stylus-Nano-Profilometer probe, rapid lateral strokes across the sample surface in a definable pattern at known high applied pressure are used to effectuate defect repair. The tip of the probe can also be dithered rapidly in a pattern or used as to create a jackhammer effect to more effectively remove material from the sample surface.