The registration and alignment of a monolayer of microdomains in a self-assembled block copolymer thin film can be controlled by chemical or physical templating methods. Although planar patterns are useful for nanoscale device fabrication, three-dimensional multilevel structures are required for some applications. We found that a bilayer film of a cylindrical-morphology block copolymer, templated by an array of posts functionalized with a brush attractive to the majority block, can form a rich variety of three-dimensional structures consisting of cylinder arrays with controllable angles, bends, and junctions whose geometry is controlled by the template periodicity and arrangement. This technique allows control of microdomain patterns and the ability to route and connect microdomains in specific directions.