A method and apparatus for forming magnetic media substrates is provided. A patterned resist layer is formed on a substrate having a magnetically susceptible layer. A conformal protective layer is formed over the patterned resist layer to prevent degradation of the pattern during subsequent processing. The substrate is subjected to an energy treatment wherein energetic species penetrate portions of the patterned resist and conformal protective layer according to the pattern formed in the patterned resist, impacting the magnetically susceptible layer and modifying a magnetic property thereof. The patterned resist and conformal protective layers are then removed, leaving a magnetic substrate having a pattern of magnetic properties with a topography that is substantially unchanged.