Embodiments described herein provide methods and apparatus for treating a magnetic substrate having an imprinted, oxygen-reactive mask formed thereon by implanting ions into a magnetically active surface of the magnetic substrate through the imprinted oxygen-reactive mask, wherein the ions do not reduce the oxygen reactivity of the mask, and removing the mask by exposing the substrate to an oxygen-containing plasma. The mask may be amorphous carbon, through which carbon-containing ions are implanted into the magnetically active surface. The carbon-containing ions, which may also contain hydrogen, may be formed by activating a mixture of hydrocarbon gas and hydrogen. A ratio of the hydrogen and the hydrocarbon gas may be selected or adjusted to control the ion implantation.