A method of making a nanotube array structure includes forming a nanorod array template on a substrate, coating a nanotube material over the nanorod array template, forming a coated template, annealing the coated template, and drying the coated template. The method then includes heating the coated template to an elevated temperature, relative to ambient temperature, at a heating rate while flowing a gas mixture including a reducing gas over the substrate at a flow rate, the reducing gas reacting with the nanorod array template and forming a gaseous byproduct and the nanotube array structure in which nanotubes may be substantially aligned with adjacent nanotubes. The nanotube array structure can be used, for example, in sensor, catalyst, transistor, or solar cell applications.