a pre - loaded plasma - based processing system comprises a pre - reaction plasma processing chamber , a power source disposed in operable communication with the pre - reaction plasma processing chamber , and a wafer plasma processing chamber disposed in fluid communication with the pre - reaction plasma processing chamber . the pre - reaction plasma processing chamber is configured to effect a plasma - based chemical reaction of reactant materials to produce a reactive radical . the wafer plasma processing chamber is configured to react the reactive radical with a species at a surface of a wafer disposed in the wafer plasma processing chamber . other embodiments include a method of processing a wafer in a plasma environment and preloading of the reactive gas stream to prevent erosion of wafer masking or etch stop layers .