Permanent nanometer structures were fabricated on chemically prepared Si by chemical activation of loosely bound hydrocarbon clusters triggered by voltage pulses across the tunneling gap of a scanning tunneling microscope. Current‐voltage measurements show that the fabrication process results in a local transition from a Schottky junction behavior to a MIS junction behavior, indicating the formation of topographic structures. Our experimental results indicate that the size and density of the clusters and the shape of the tunneling tip are important factors of the process. An example of parallel fabrication is presented.