Novel processes have been developed for transferring patterns using self-assembled monolayer (SAM) electron beam resists. Because the SAMs are very thin, high-selectivity processes are required for effective substrate modification. Two separate techniques have been studied for patterning intermediate layers for use as reactive ion etch (RIE) masks. A bilayer process using the native oxide as an intermediate etch mask has been used to etch into both crystalline and polycrystalline silicon. The native oxide is patterned with the SAM resist and the oxide is then used as a mask in an electron cyclotron resonance RIE. This process has been used to produce similar to 25 nm etched features in silicon. Instead of its selective removal, an alternative technique for forming the intermediate etch mask layer is the selective deposition of the layer. Thin nickel layers have been formed with an electroless plating technique on silicon. The electroless deposition is highly selective for producing nickel plating on silicon as opposed to the silicon oxide. These novel high-selectivity techniques demonstrate the ability for ultrathin SAM resist layers to pattern silicon and other materials.