A patterned perpendicular magnetic recording medium of the type that has spaced-apart pillars with magnetic material on their ends and with trenches between the pillars that are nonmagnetic regions is made with a method that allows use of a pre-etched substrate. A nonmagnetic capping layer is located in the trenches above the nonmagnetic regions. The substrate has diffusion material in the trenches that when heated will diffuse into the magnetic recording layer material and chemically react with it. The pillars are formed of material that will not diffuse into the recording layer. The recording layer is formed over the entire substrate and a nonmagnetic capping layer that is not chemically reactive with the diffusion material is formed over the recording layer in the trenches. The substrate is annealed to cause the recording layer material in the trenches and the material in the substrate to diffuse into one another and chemically react to render the trenches nonmagnetic. The capping layer suppresses the diffusion of material from the substrate to the surface in the trenches and thus prevents migration of diffusion material to the recording layer material on the ends of the pillars.