Directed assembly provides a method to generate nanoscale materials with intrinsic electronic, optical, and magnetic properties. The approach combines self-assembly (bottom-up approaches) with current top down techniques to create nanoscale materials. Noncovalent interactions, such as hydrogen bonding, electrostatics, and π-stacking, can be used spatially to guide molecules into supramolecular or nanoscale complexes. This thesis demonstrates new nanofabrication methods, starting with relatively simple interactions, such as host-guest chemistry, and proceeding to more complex nanoscale materials. Chapter 1 provides a general overview of the motivation behind nanofabrication techniques. Chapter 2 provides a fundamental understanding of noncovalent interactions and their use within bottom-up approaches. Chapter 3 cites specific host-guest chemistry of an azobenzene flavin moiety that tunes the optical properties of the push-pull system. Chapter 4 provides a method to assemble organic nanowires through cooperative dipolar and hydrogen bonding interactions. And finally, Chapter 5 facilitates the combination of bottom-up and top down approaches by introducing nanoimprinted polymer patterns as self-assembly templates.