A method of forming an aligned connection between a nanotube layer and a raised feature is disclosed. A substrate having a raised feature has spacers formed next to the side of the raised feature. The spacers are etched until the sidewalls of the raised feature are exposed forming a notched feature at the top of the spacers. A patterned nanotube layer is formed such that the nanotube layer overlies the top of the spacer and contacts a side portion of the raised feature in the notched 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.