Method and apparatus for forming a patterned magnetic substrate are provided. A patterned resist is formed on a magnetically active surface of a substrate. An oxide layer is formed over the patterned resist by a flowable CVD process. The oxide layer is etched to expose portions of the patterned resist. The patterned resist is then etched, using the etched oxide layer as a mask, to expose portions of the magnetically active surface. A magnetic property of the exposed portions of the magnetically active surface is then modified by directing energy through the etched resist layer and the etched oxide layer, which are subsequently removed from the substrate.