Nanoimprint lithography (NIL) is used as a tool to pattern self-assembled monolayers (SAMs) on silicon substrates because of its ability to pattern in the micrometer and nanometer ranges. The polymer template behaves as a physical barrier preventing the formation of a SAM in the covered areas of the substrate. After polymer removal, SAM patterns are obtained. The versatility of the method is shown in various nanofabrication schemes. Substrates are functionalized with a second type of silane adsorbate. Pattern enhancement via selective electrostatic attachment of carboxylate-functionalized particles is achieved. Further applications of the NIL-patterned substrates include template-directed adsorption of particles, as well as the fabrication of electrodes on top of a SAM.