A method of forming a superconductor structure is provided. The method comprises forming a superconducting element in a first dielectric layer that has a top surface aligned with the top surface of the first dielectric layer, forming a second dielectric layer over the first dielectric layer and the superconducting element, and forming an opening in the second dielectric layer to a top surface of the superconducting element. The method also comprises performing a cleaning process on the top surface of the superconducting element to remove oxides formed on the top surface of the superconducting element at a first processing stage, forming a protective barrier over the top surface of the superconducting element, and moving the superconductor structure to a second processing stage for further processing.