The fabrication of nanostructures with controlled assembly and architecture is very important for the development of novel nanomaterial-based devices. We demonstrate that laser techniques coupled with low-temperature hydrothermal growth enable complex three-dimensional ZnO nanorod patterning on various types of substrates and geometries. This methodology is based on a procedure involving the 3D scaffold fabrication using Multi-Photon Lithography of a photosensitive material, followed by Zn seeded Aqueous Chemical Growth of ZnO nanorods. 3D, uniformly aligned ZnO nanorods are produced. The increase in active surface area, up to 4.4 times in the cases presented here, provides a dramatic increase in photocatalytic performance, while other applications are also proposed.