A perpendicular magnetic recording (PMR) disk has a patterned template layer for the growth of the magnetic grains and the nonmagnetic material surrounding the grains. The template layer is a substantially planar platinum (Pt) or palladium (Pd) layer that is patterned to have Pt or Pd regions arranged in a hexagonal-close-packed (hcp) pattern with the Pt or Pd regions surrounded by Pt-oxide or Pd-oxide regions. The two separate regions of the template layer have different surface chemistries and energies, which provide a “chemical contrast” to impinging atoms during deposition of the metallic magnetic material and nonmagnetic (typically oxide) material, effectively guiding the deposition. The metallic magnetic material is preferentially deposited on the pristine, epitaxial Pt or Pd regions to form the magnetic grains, while the oxide migrates to the oxidized Pt or Pd regions due to the matching of lower surface energy.