Low-energy proton irradiation was applied to pattern an array of metallic, ferromagnetic nanoislands through the local phase transformation of an oxidic, paramagnetic phase in a complex superlattice composed of repetitions of an oxidic and metallic layer. The irradiation inflicted minimal damage on the structure, resulting in the absence of unwanted defects and side effects. This nondestructive pattern transfer was clearly confirmed by the contrast between irradiated and unirradiated regions in electrical, chemical, and magnetic images. Simulation based on the magnetic properties suggests that this low-energy proton irradiation can nondestructively pattern an array of ferromagnetic islands with 8.2 nm in diameter and 7.4 nm in spacing between islands, which means it can achieve an areal density of ∼3 Tb/in.(2) with a thermal stability of over 80 kBT. Such an array is strong enough to overcome the so-called superparamagnetism limit in magnetic recording. The attributes demonstrated here corroborate that proton irradiation can be applied to design and pattern devices on a nanometer scale not only for magnetic but also for electric and optical materials systems in all such systems in which a local phase transformation is available.