Nanoimprint lithography is used to create large-area two-dimensional prepatterns with tunable topographic heights in a resist layer. The resist prepatterns are applied to direct the self-assembly of sphere-forming polystyrene-block-polydimethylsiloxane block copolymers so as to form sparse nonregular nanodot arrays with flexible pattern layouts from high-topography prepattern or dense regular nanodot arrays with a multiplicative pattern density from low-topography prepattern. By precisely controlling the topographic height in substrate prepatterns, the origin of directed self-assembly of block copolymer spheres using low-topography prepattern is found to be topographic contrast. High-fidelity pattern transfer from spherical block copolymer nanotemplates to functional materials indicates a promising route to ultrahigh density nanodevices. Bit-patterned media over 1 teradot/in on a 2.5-inch disk are fabricated, thus presenting future magnetic data storage media with great areal density growth potential. (c) 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 361-367