Nano-patterning on the order of sub-10 nm is integral to achieve high-density nano-scale devices for various data storage and data processing applications. However, the additional requirement of planarization and unwanted side-effects of physical or chemical etching have so far limited the patterning of sub-10 nm devices. In this work, we have demonstrated the creation of an array of ∼10 nm ferromagnetic islands through selective phase transformation of paramagnetic multilayers by low-energy proton irradiation. Paramagnetic Co3O4/Pd multilayers masked with patterned PMMA (polymethyl methacrylate) were reduced to ferromagnetic Co/Pd by proton irradiation. A clear contrast of the nano-islands was observed using magnetic force microscopy, establishing the formation of ferromagnetic nano-islands with perpendicular magnetic anisotropy. This process provides a way to circumvent the side-effects associated with both conventional nano-scale pattering and high-energy ion irradiation. Therefore, phase transformation by low energy proton irradiation can be used for patterning sub-10 nm nano-islands, not only for magnetic data storage but also for patterning various opto-electronic and spintronic devices.