Embodiments of methods for removing carbon-containing films are provided herein. In some embodiments, a method for removing a carbon-containing layer includes providing an ammonia containing process gas to a process chamber having a substrate with a silicon oxide layer disposed atop the substrate and a carbon-containing layer disposed atop the silicon oxide layer disposed in the process chamber; providing RF power to the process chamber to ignite the ammonia containing process gas to form a plasma; and exposing the substrate to NH and/or NH2 radicals and hydrogen radicals formed in the plasma to remove the carbon-containing layer.