We have used a variety of self-assembled monolayers as resists for low energy electron beam patterning. These compounds can be used as high-resolution patternable linker molecules for selected area binding of proteins and other organic compounds, as well as nanoparticles with organic chemical coatings. Because these systems can be aligned in registry to existing patterns, the organic systems may be positioned with the accuracy of electron-beam lithography. We have also explored the use of self-assembled monolayers for the creation of sub-wavelength artificial dielectric systems. The ultra-thin patterned monolayer is combined with a contrast-enhancing etch process to create high aspect ratio structures. This technique can be used to fabricate diffractive optical devices in a single-step process.