Programmable nanotube interconnect is disclosed. In one embodiment, a method includes forming a interconnect layer using a plurality of nanotube structures, and automatically altering a route of an integrated circuit based on an electrical current applied to at least one of the plurality of nanotube structures in the interconnect layer. Neighboring interconnect layers separated by planar vias may include communication lines that are perpendicularly oriented with respect to each of the neighboring interconnect layers. The nanotube structure may be chosen from a group comprising a polymer, carbon, and a composite material. A carbon nanotube film may be patterned in a metal layer to form the plurality of nanotube structures. A sputtered planar process may be performed across a trench of electrodes to create the carbon nanotube structures.