Directed self-assembly of block copolymers offers a novel paradigm for building up three-dimensional (3D) device-oriented nanostructures towards deep sub-100-nm resolution. To clearly unveil the 3D patterns with long-range order, we herein utilize computer simulations to explore the directed self-assembly behaviors of cylindrical-forming block copolymer films in topographical templates. Unlike the 3D architectures in the bulk, the cylinder orientations in various layers of 3D ordered structures are independently manipulated by modulating the design parameters of topographical templates. Moreover, a set of design strategies are proposed to precisely construct the 3D non-trivial structures with T-junctions and jogs at desired locations and layers. Importantly, the simulations clarify the experimental observations about the formation range of 3D interconnected structures, and manifest that the vertical interconnections depend strongly on the template thickness. These results provide detailed insights into the nature of 3D assembled structures, and furthermore offer promising strategies for constructing the 3D device-oriented elements such as T-junctions, jogs and interconnections. (C) 2015 Elsevier Ltd. All rights reserved.