A highly versatile and scalable path to obtain buried magnetic nanostructures within alloy thin films, while maintaining a flat topography, is described. A magnetic pattern of nanoscale periodicity is generated over ∼cm2 areas by employing a B2 → A2 structural transition in the prototype Fe60Al40 thin alloy films. The phase transition was induced in the confined regions via ion-irradiation through self-assembled nanosphere masks. In this way, large area patterns of a hexagonal symmetry of ferromagnetic nanostructures embedded within a paramagnetic Fe60Al40 thin film are realized. The depth and lateral distribution of the induced magnetization was investigated by magnetometry and microscopy methods. Magnetic contrast imaging as well as simulations shows that the obtained magnetic structures are well defined, with the magnetic behavior tunable via the mask geometry.