A method is provided of forming a superconductor device interconnect structure. The method includes forming a first dielectric layer overlying a substrate, and forming a superconducting interconnect element in a first dielectric layer, such that the superconducting interconnect element has a top surface aligned with a top surface of the first dielectric layer to form a first interconnect layer. The method also includes performing a plasma clean on a top surface of the first interconnect layer, and depositing a second dielectric layer over the first dielectric layer.