We have used ion beam irradiation through a silicon stencil mask to alter the magnetic properties of Co/Pt multilayer and FePt chemically-ordered superlattice films. In both systems, ion irradiation disorders the as-grown films which results in a reduction of the magnetic anisotropy. Regularly spaced micrometer-sized regions of magnetically altered material have been produced over areas of a square millimeter. These magnetic structures have been observed by magnetic force microscopy. By stepping the mask during irradiation, features at twice the spatial frequency of the mask holes have been produced. Such patterned magnetic films are of interest for application in high-density magnetic recording.