We report on the thin film self-assembly and post fabrication functionalization of cylinder-forming poly(styrene-block-2-vinyl-4,4-dimethylazlactone) (PS-b-PVDMA) block copolymers (BCPs). Thermal annealing of an asymmetric BCP composition, to drive microphase separation in thin films, results in high defect densities and poor long-range order. Using FTIR spectroscopy and ellipsometry, we demonstrate that thermal annealing results in reactions between the azlactone groups and the underlying substrate leading to BCP "pinning". We demonstrate that solvent annealing circumvents these issues and drives high fidelity microphase separation of the BCP in thin films. The solvent annealing approach also enables control over domain orientation; we show that parallel and perpendicularly oriented cylinders with diameters of 11.7 +/- 1.2 nm and a center to-center distance of 25.2 +/- 2.6 nm can be obtained using a BCP with M-n = 29.5 kDa and f(s) = 0.75. The PVDMA segments in these self-assembled thin films remain available for reaction with primary amine-functionalized nucleophiles. X-ray photoelectron spectroscopy (XPS) depth-profiling reveals that reactions between azlactone groups and incoming amines occur primarily in the top few nanometers of the reactive domains. Finally, we demonstrate that the azlactone groups in both parallel and perpendicularly oriented cylindrical thin films can selectively incorporate trimethylaluminum vapor, which can be subsequently converted into Al2O3 nanowires and nanodots with dimensions of 16 and 12 nm, respectively.