Chemical reactions of terminal functional groups of organosiloxane surface assemblies were induced by a catalytically active palladium-coated atomic force microscopy (AFM) tip, resulting in lithographed patterns with minimum measured line widths of 33 nm. We describe three schemes: Pd-catalyzed transfer hydrogenation on terminal azide and carbamate (CBZ-amino) functional groups and Pd-catalyzed addition of aminobutyldimethylsilane on the terminal alkene bond of N-octenyldimethylsiloxane surface assemblies. The minimum applied force required to cause chemical change in the end functional groups is approximately 2.5 muN, and detectable amounts of chemical conversion occurred at raster scan rates up to 5 mum/s. Physical dislocation of the surface assembly competes with chemical writing, but this can be alleviated by strong covalent attachment of the surface assembly to substrate (i.e., by complete condensation of assembling silanols to siloxane bridges). For the strongest trialkoxysilane-derived surface assemblies, virtually complete physical dislocation of the surface assembly occurs at 7.6 muN. Each chemical writing scheme described in this paper results in terminal amine functional groups which are labeled with fluorescent probes. Features are imaged with confocal and atomic force microscopy. Labeling via covalent attachment of biotin, followed by attachment of streptavidin-coated gold nanoparticles, also gave evidence of chemical conversion.