A method and apparatus for forming a magnetic layer having a pattern of magnetic properties on a substrate is described. The method includes using a metal nitride hardmask layer to pattern the magnetic layer by plasma exposure. The metal nitride layer is patterned using a nanoimprint patterning process with a silicon oxide pattern negative material. The pattern is developed in the metal nitride using a halogen and oxygen containing remote plasma, and is removed after plasma exposure using a caustic wet strip process. All processing is done at low temperatures to avoid thermal damage to magnetic materials.