Ultra thin complex multilayer structures have many potential applications in molecular and organic electronics, sensing, biotechnology and other areas. Reported here is a method by which to construct multifunctional, multilayer, patterned structures, using alkanethiolate SAMs adsorbed on Au, UV photopatterning, and chemoselective covalent bond formation. We demonstrate that amide coupling is efficient for producing multilayer structures on -COOH-terminated SAMs. while oxime coupling is efficient for producing multilayer structures on -CHO-terminated SAMs. Reaction yields obtained are similar to 67% and similar to 84% for the coupling of the first layer (bilayer formation) for amide and oxime coupling, respectively. Subsequent ad layer formation occurs with similar to 100% yield in both cases. The resulting ad layers are chemically robust and arc suitable for subsequent chemical processing. Finally, both chemistries are used to produce a complex multilayer structure atop a UV photopatterned SAM. The resulting construct is well-defined and has the same lateral resolution as the photopatterned SAM substrate. The method demonstrated here is synthetically flexible and allows for the assembly of functionally complex surfaces and, in principle, the incorporation of biomolecules and metals.