It is common to electrochemically cycle catalysts prior to testing to remove contaminants that are left on the surface of the catalysts due to synthesis or exposure to ambient atmosphere. We discuss a new electrochemical pretreatment cleaning protocol for ORR catalysts that exposes the catalysts to higher potentials and demonstrate this procedure on a class of Ru@Pt core-shell catalysts that we have recently developed. After treatment with the new cleaning protocol, the Ru@Pt catalysts show a 30mV improvement in halfwave potential, and changes in the baseline nitrogen CVs. The changes in the baseline CVs indicate a more complete removal of surface contaminants and atomic restructuring, both of which could account for the improved activity. Additionally, we show that inaccuracies in measurements of the electrochemical surface area by Hupd are rectified by the new cleaning protocol.