Block copolymer self assembly presents a method for patterning and templating applications on the 10-50 nm length scale, a smaller scale than can be easily achieved by photolithography. Here we investigate the use of functionalized polar-nonpolar block copolymers both as photopatternable self-assembling materials and for selective infiltration of one block for patterning. Block copolymer thin films with defect-free self-assembled morphology over large domains combined with careful control of the orientation of the morphology are critical for these patterning applications. Self assembly of block copolymers is facilitated by polymer chain mobility, commonly achieved by heating block copolymer films above the glass transition temperature of the blocks. However, many block copolymer systems, including those discussed here, are thermally incompatible. Swelling in a solvent vapor, called solvent annealing, provides sufficient mobility for self assembly. Solvent annealing proved critical to forming ordered structures of functional polar-nonpolar block copolymer thin films. Thermal instability initially led to limited self assembly of combined topdown/bottom-up block copolymer systems. In this case, photolithographic functionality has been designed into block copolymers, allowing the majority component of a block copolymer to behave as a negative-tone photoresist. Solvent vapor annealing has provided a simple and inexpensive method for allowing the bottom-up self assembly of these top-down photopatternable materials. An additional benefit of solvent annealing is the ability to reversibly tune the morphology formed using the selectivity of different swelling solvents to the two blocks: that is, the choice of solvent for annealing directs the formation of different morphologies in the dried film, here spherical and cylindrical. This behavior is reversible, alternating annealing sessions lead to switching of the morphology in the film. Secondary ordering techniques applied in tandem with solvent annealing can be used to further control the self assembly and give highly ordered block copolymer domains. Here we demonstrate the use of graphoepitaxy to align block copolymer self assembly to patterns in substrates. The combination of block copolymer self assembly with lithographic crosslinking in films was initially pursued to allow precise location of assembled patterns. Taking this behavior a step further, we combine solvent annealing, used to reversibly tune the self-assembled morphology, and lithographic patterning, used to prevent switching in exposed regions. This combined process has provided a method for selectively patterning 100 nm-wide domains of spherical morphology within regions of parallel-oriented cylindrical morphology. We also investigate solvent annealing of a block copolymer blended with a hydrogen bonding material that selectively segregates into the polar block. Blending provides a method of tuning the periodicity upon solvent annealing for self assembly, with morphology control again possible by solvent selectivity. Selective extraction of the blended material forms voids displaying the tunable periodicity, and the pattern is then transferred by templating to inorganic materials.