This paper describes an approach to fabricate organic molecular films patterned with a lateral resolution of up to a few tens of nanometers. These films were formed onto specific sites that were prepared with precise geometrical and chemical control on silicon (Si) substrates. Nanolithographic methods based on scanning probe anodization, a surface modification technology which uses electrochemical reactions induced in adsorbed water confined beneath a tip of a scanning probe microscope, were applied to prepare anodic Si oxide (SiOx) or gold (Au) nanostructured patterns on the Si substrates. These substrates were then exposed to trimethylchlorosilane (TMCS) vapor or n-hexadecyl mercaptan (HDM) liquid, respectively. Nano-scale patterns of organic monolayer films were formed on these substrates due to the site-selective chemisorption of the precursor molecules, that is, TMCS to SiOx or HDM to Au. Evidence that the corresponding organic monolayers were grown area-selectively onto the SiOx and Au was obtained using an atomic/lateral force microscope and a scanning Auger nanoprobe.