Mechanically stable monolayers with chemically functional patterns are fabricated by the combination of spatially resolved chemical lithography with complete cross-linking of aromatic self-assembled monolayers (SAMs). The process starts with a local electron exposure of a SAM of 4'-nitro-1,1'-biphenyl-4-thiol that converts the nitro into amino groups and, additionally, generates a pattern of cross-linked and non cross-linked regions. In the next step, molecules in the non cross-linked regions are exchanged for 1,1'-biphenyl-4-thiol. A subsequent electron exposure cross-links these regions, yielding a fully cross-linked, chemically patterned SAM. The reverse process that generates chemically complementary patterns is also demonstrated. For both processes, X-ray photoelectron spectroscopy and atomic force microscopy are used to monitor the fabrication steps and to determine the kinetics of the thiol exchange. The functionality of the fully cross-linked, chemically patterned monolayer is tested by the site selective derivatisation with pentanoic acid chloride.