Disclosed is a structure made of a trench patterned substrate having a pre-determined trench period and a pre-determined mesa to trench width ratio, and a block copolymer on top of the trench patterned substrate. The block copolymer has at least an organic block and a silicon-containing block, wherein the block copolymer can have either perpendicular or parallel cylinders. The structure is annealed under a pre-determined vapor pressure for a predetermined annealing time period, wherein the pre-determined trench period, the pre-determined mesa to trench width ratio, the predetermined vapor pressure and the predetermined annealing time period are chosen such that cylinders formed in the block copolymer are either perpendicular or parallel with respect to the trench-patterned substrate. A method is also described to form the above-mentioned structure.