Minute patterns have been fabricated on organosilane self‐assembled monolayers (SAMs) based on scanning probe surface modification. An SAM was prepared on Si substrates from an organosilane precursor. First, using an atomic force microscope (AFM) with a conductive probe, current was injected from the probe into the SAM‐covered Si substrate so that the SAM was locally degraded at the probe‐contacting point. The patterning could be conducted in air while, in vacuum at the order of 10−6Torr, or in an atmosphere purged with nitrogen, no detectable patterns were fabricated. The presence of adsorbed water at the probe/sample junction was confirmed to be crucial for the patterning of the SAM/Si. Its mechanism was, thus, ascribed to electrochemical reactions of the SAM with adsorbed water. Furthermore, we demonstrated the chemical conversion of terminal functional groups on the SAM by the current injecting AFM. The results were confirmed through surface potential imaging by Kelvin probe force microscopy and a chemical labeling method. An SAM terminated with −CH3groups was found to be converted to a COOH‐terminated SAM due to anodic oxidation. The tip‐induced electrochemical reduction from −NO to −NH2was successfully conducted as well. Both the oxidation and reduction reactions have been shown applicable to scanning probe surface modification. © 2003 American Institute of Physics