The control of order and orientation of the self-assembly of cylinder-forming poly(styrene-b-dimethylsiloxane) block copolymer is demonstrated. Copolymer thin films are spun-cast onto topographically patterned (well-defined rectangular cross-section channels) polyhedral-silsesquioxane-type resist templates and annealed in solvent vapor. The templates used here are fabricated by UV-curing nanoimprint lithography and the surface properties of the resist are tuned by the ligands coordinated to the resist's silsesquioxane cages. Depending on the resist's composition and on the surface chemistry at the base of the trench (resist or silicon), various morphologies and orientations of the polydimethylsiloxane cylinders are observed without the use of a brush layer. Some surfaces are demonstrated to be neutral for the copolymer, without any wetting layer and, under favorable conditions, highly ordered features are observed over substrate areas of about 1 cm2 (scalable to larger surfaces). Also, the possibility of using solvents widely accepted in industry for polymer spin-coating and annealing is proved. Due to the high plasma etch resistance of the polydimethylsiloxane block, self-assembled patterns can be transferred to the silicon substrate producing silicon features with aspect ratios up to 2. We demonstrate that the methodology developed here could be integrated into conventional fabrication processes and scaled to wafer production. © 2013 The Royal Society of Chemistry.