A method of forming a self-aligned logic cell. A nanotube layer is formed over the bottom electrode. A clamp layer is formed over the nanotube layer. The clamp layer covers the nanotube layer, thereby protecting the nanotube layer. A dielectric layer is formed over the clamp layer. The dielectric layer is etched. The clamp layer provides an etch stop and protects the nanotube layer. The clamp layer is etched with an isotropic etchant that etches the clamp layer underneath the dielectric layer, creating an overlap of the dielectric layer, and causing a self-alignment between the clamp layer and the dielectric layer. A spacer layer is formed over the nanotube layer. The spacer layer is etched except for a ring portion around the edge of the dielectric layer. The nanotube layer is etched except for portions that are underlying at least one of the clamp layer, the dielectric layer, and the spacer layer, thereby causing a self-alignment between the clamp layer, the overlap to the dielectric layer, the spacer layer, and the nanotube layer.