Three-dimensional Network-on-Chip (3-D NoC) is an emerging research area exploring the network architecture of 3-D ICs that stack several smaller wafers or dice for reducing wire length and wire delay. Various network topologies such as meshes, tori, and trees have been used for NoCs. In particular, much attention has been focused on tree-based topologies, such as Fat Trees and Fat H-Tree, because of their relatively short hop-count that enables lower latency communication compared to meshes or tori. However, since on-chip tree-based networks in their 2-D layouts have long wire links around the root, they generate serious wire delay, posing severe problems to modern VLSI design. In this paper, we propose a 3-D layout scheme of trees including Fat Trees and Fat H-Tree for 3-D ICs in order to resolve the trees' intrinsic disadvantage. The 3-D layouts are compared with the original 2-D layouts in terms of network logic area, wire length, wire delay, number of repeaters inserted, and energy consumption. Evaluation results show that 1) total wire length is reduced by 25.0% to 50.0%; 2) wire delay is improved and repeater buffers that consume considerable energy can be removed; 3) flit transmission energy is reduced by up to 47.0%; 4) area overhead is at most 7.8%, which compares favorably to those for 3-D mesh and torus.