A method of forming an aligned connection between a nanotube layer and an etched feature is disclosed. An etched feature is formed having a top and a side and optionally a notched feature at the top. A patterned nanotube layer is formed such that the nanotube layer contacts portions of the side and overlaps a portion of the top of the etched feature. The nanotube layer is then covered with an insulating layer. Then a top portion of the insulating layer is removed to expose a top portion of the etched feature.