A nanopatterning process, named as the embedded mask patterning, was proposed and experimentally demonstrated based on the FePt recording media. A granular mask layer was deposited on top of a FePt continuous film. The granular pattern of the mask was then transferred down to FePt layer using reactive ion etching. Since controlling magnetic properties is separated from controlling granular nanostructure, FePt grains can be reduced by optimizing the mask layer and patterning process only. This process is also potentially compatible to any state-of-art vacuum process for other electronic devices wafers and heterostructured nanoparticles manufacturing.