A method for making a bit-patterned-media (BPM) magnetic recording disk includes depositing a FePt (or CoPt) alloy recording layer, and then depositing a sealing layer on the FePt layer before high-temperature annealing. The high-temperature annealing causes the FePt to become substantially chemically-ordered in the L10 phase. After annealing, the sealing layer is removed. The sealing layer prevents nanoclustering and agglomeration of the FePt material at the surface of the FePt layer and the sealing layer, which would result in undesirable high surface roughness of the FePt, making patterning of the FePt layer difficult. The FePt layer can be patterned into the discrete islands for the BPM disk either before deposition of the sealing layer or after deposition and removal of the sealing layer. After patterning and removal of the sealing layer, the disk protective overcoat is deposited over the discrete data islands.