This work demonstrates a simple approach to control the orientation of the self-assembled nanostructured block copolymer thin films of polystyrene-block-polydimethylsiloxane (PS-b-PDMS) by functionalization of the oxide layer (SiO2) on the Si substrate followed by thermal annealing under low-pressure environmental conditions. The substrate can be functionalized through two-step grafting of hydroxy-terminated polystyrene brush (PS–OH brush) followed by hydroxy-terminated polydimethylsiloxane brush (PDMS–OH brush) onto the wafer substrate. By controlling the grafting ratio of PS–OH and PDMS–OH brushes, the affinities of the PS and PDMS blocks with the substrates can be fine-tuned to provide a neutral substrate in order to form perpendicular cylinders from the bottom after thermal annealing. Owing to the vacuum-driven orientation [i.e., thermal annealing under low-pressure environment conditions (∼10–4 Pa)], the orientation of the cylinders can be controlled at the air/polymer interface. Interestingly, by combining the vacuum-driven approach with substrate functionalization, perpendicular cylinders from the air/polymer interface and substrate/polymer interface can be generated, respectively. Consequently, well-aligned perpendicular cylinders with long-range ordering can be fabricated by the self-alignment process.