We present a method of direct magnetic patterning of a nonmagnetic Co-C amorphous film by electron beam radiation induced nano-scale phase transition. Co-C alloy films with C concentration from 30 to 50 at% and thickness of 30-60 nm were prepared by alternately sputtering Co and C films onto C-buffered glass substrates. The films are amorphous and nonmagnetic with C concentration up to 40 at%. Due to their negative mixture entropy, as-deposited amorphous Co-C alloy films are metastable. Focused electron-beam irradiation causes localized phase segregation of the immiscible magnetic (Co-rich) and nonmagnetic (C-rich) phases. Ferromagnetic Co(C) nano-dot array was fabricated by subjecting the as-deposited Co 60C 40 films to electron beam radiation using a beam current of 16 nA, a beam energy of 20 keV and a dwell time of 5 s per dot. Magnetic force microscopy images and magnetic measurements confirm the formation of the ferromagnetic phase. The present single-step nanolithography eliminates the cumbersome traditional processes and is potentially a new and flexible alternative for fabricating patterned magnetic nanostructures for submicron magnetic devices.