We have developed a robust method by which to construct complex two- and three- dimensional structures based on controlling interfacial chemistry. This work has important applications in molecular/organic electronics, sensing, and other technologies. Our method is extensible to many different materials, easily parallelized, affords precise nanoscale placement and is fully compatible with photolithography. Our work to date has provided a simple method for the construction of complex 2D molecular electronic circuitry using UV-photopatterning and the reaction of deposited metals with self-assembled monolayers (SAMs). To demonstrate the method we have selectively vapor-deposited Mg on a patterned -CH@sub 3@/-COOH terminated alkanethiolate surface. The deposited metal penetrates through the -CH@sub 3@ SAM to the Au/S interface while reacting with and accumulating on top of the -COOH SAM. Applying these ideas to the rational design of metal/organic structures requires a fundamental understanding of the underlying metal-molecule interactions; we therefore shall also discuss experiments that elucidate these.