We report a method to fabricate high-quality patterned magnetic dot arrays using block copolymer lithography, metal deposition, and a dry lift-off technique. Long-range order of cylindrical domains oriented perpendicular to the substrate and in hexagonal arrays was induced in the block copolymer films by prepatterning the substrate with topographic features and chemically modifying the surface to exhibit neutral wetting behaviour towards the blocks of the copolymer. The uniformity of the domain size and row spacing of block copolymer templates created in this way was improved compared to those reported in previous studies that used graphoepitaxy of sphere-forming block copolymers. The pattern of block copolymer domains was transferred to a pattern of magnetic metal dots, demonstrating the potential of this technology for the fabrication of patterned magnetic recording media.