An opening in a substrate is formed, e.g., using optical lithography, with the opening having sidewalls whose cross section is given by segments that are contoured and convex. The cross section of the opening may be given by overlapping circular regions, for example. The sidewalls adjoin at various points, where they define protrusions. A layer of polymer including a block copolymer is applied over the opening and the substrate, and allowed to self-assemble. Discrete, segregated domains form in the opening, which are removed to form holes, which can be transferred into the underlying substrate. The positions of these domains and their corresponding holes are directed to predetermined positions by the sidewalls and their associated protrusions. The distances separating these holes may be greater or less than what they would be if the block copolymer (and any additives) were to self-assemble in the absence of any sidewalls.