This article describes the use of scanning catalytic probe lithography for nanofabrication of patterns on self-assembled monolayers (SAMs) of reactive adsorbates. Catalytic writing was carried out by scanning over bis(-tert-butyldimethyl-siloxyundecyl)disulfide SAMs using 2-mercapto-5-benzimidazole sulfonic acid-functionalized gold-coated AFM tips. The acidic tips induced local hydrolysis of the silyl ether moieties in the contacted areas, and thus patterned surfaces were created. Diffusion effects arising from the use of an ink were excluded in these type of experiments, and therefore structures with well-defined shapes and sizes were produced. The smallest lines drawn by this technique were about 25 nm wide, corresponding to the actual contact area of the tip. Lateral force microscopy studies performed on different SAMs helped to clarify the nature and cause of the friction contrasts observed by AFM. Dendritic wedges with thiol functions inserted into the catalytically written areas, thus enhancing the height contrast. The created patterns open possibilities to build 3D nanostructures.