Carbon nanotubes are a nanostructured material that promises to have a wide range of applications. However, the present techniques used to build nanotube architectures have several deficiencies, such as the inability to precisely and controllably align the nanotubes. This invention is a novel and powerful method to assemble carbon nanotubes on planar substrates to build and control highly organized 1-to-3D architectures. The growth of aligned multi-walled nanotubes in patterns and in multiple directions has been demonstrated on lithographically machined templates of oxidized silicon surfaces in a single process, carried out through a proprietary CVD process. Carbon nanotubes grow normal to and selectively on silica while not forming on the oxidized silicon, and the nanotubes inherit the topography of the substrate templates. This bottoms-up controlled fabrication approach is straight forward, scalable, and compatible with silicon micro-fabrication laboratory equipment.