A method for cleaning contacts on a substrate incorporates ion control to selectively remove oxides. The method includes exposing the substrate to ions of an inert gas, supplying a first RF frequency of a first bias power supply to a substrate support, supplying a second RF frequency of a second bias power supply to a substrate support, and adjusting a first power level of the first RF frequency and a second power level of the second RF frequency to selectively remove oxide from at least one contact on the substrate while inhibiting sputtering of polymer material wherein the oxide removal is selective over removal of polymer material surrounding the at least one contact.