Embodiments of the present invention provide a manufacturing method that can form a track guide separation area of a magnetic disk substrate constituting a patterned medium represented by a discrete track medium or bit patterned medium suitable for high recording density, uniformly on the whole surface of the magnetic disk substrate, and accurately according to the mask. According to one embodiment, a soft magnetic film, an under coating film, and a magnetic film are formed on a substrate. A mask having an arbitrary pattern shape provided for forming the track guide separation area in the magnetic film is formed on the magnetic film, and the track guide separation area is formed by irradiating ions and electrons onto the surface of the magnetic film and applying an intermittent voltage to the substrate, thereby non-magnetizing the area irradiated.