Techniques that can produce patterns with nanoscale details on surfaces have a central role in the development of new electronic(1-3), optical(4-6) and magnetic(7-10) devices and systems. High-energy ion irradiation can produce nanoscale patterns on ferromagnetic films by destroying the structure of layers or interfaces(10-18), but this approach can damage the film and introduce unwanted defects(13,14). Moreover, ferromagnetic nanostructures that have been patterned by ion irradiation often interfere with unpatterned regions through exchange interactions, which results in a loss of control over magnetization switching(15-18). Here, we demonstrate that low-energy proton irradiation can pattern an array of 100-nm-wide single ferromagnetic domains by reducing [Co3O4/Pd](10) (a paramagnetic oxide) to produce [Co/Pd](10) (a ferromagnetic metal). Moreover, there are no exchange interactions in the final superlattice, and the ions have a minimal impact on the overall structure, so the interfaces between alternate layers of cobalt (which are 0.6 nm thick) and palladium (1.0 nm) remain intact. This allows the reduced [Co/Pd](10) superlattice to produce a perpendicular magnetic anisotropy that is stronger than that observed in the metallic [Co/Pd](10) superlattices we prepared for reference. We also demonstrate that our non-destructive approach can reduce CoFe2O4 to metallic CoFe.