This paper investigates the structural characteristics of templated synthetic anti-ferromagnetic (SAF) magnetic nanoparticles fabricated on two different release layers. When copper was used as the latter, the layered structure of the SAFs was found to be disrupted with wavy multi-layers due to the formation of copper grains from the release layer. By introducing oxygen into the copper release layer before the deposition of the film, the topography of the oxidized copper grains was effectively controlled. This led to the fabrication of SAF nanoparticles with flat multi-layers.