We demonstrate a method for controlling whether the block copolymer (BCP) cylinders comprising a thin film self-assembled on a Si substrate are oriented parallel or vertical to the substrate. This was accomplished by fabricating topographic patterns having different trench/mesa ratios on the Si substrate and resulting in the dewetting behavior of the BCP film on the mesa regions of the substrate, which led to the migration of the BCP mass from the mesas to the trenches owing to capillary forces during thermal annealing. By increasing the width of the mesas, the thickness of the BCP films formed in the trenches could be increased. Thus, by increasing the trench/mesa ratio from 1 : 1 to 1 : 3, the thickness of the BCP film in the trenches could be increased with precision from 18 to 26 nm. Films comprising arrays of parallelly oriented cylinders were preferentially formed with thicknesses of less than 21.5 nm. For films greater than 22.5 nm in thickness, the orientation of the cylinders switched and the cylinders became vertically oriented in the absence of interfacial sublayers between the BCP film and the topographic guide patterns on the Si substrate.