The structure and properties of nanoscale magnetic island arrays for bit patterned media (BPM) have been studied. A periodic Si nano-island array was fabricated by nano-imprint-lithography (NIL), with the trench-filling and flattening achieved by resist spin coating followed by reactive ion back-etching. A Co/Pd multilayer magnetic media with a perpendicular anisotropy was then sputtered and lifted-off so that the processed nanostructure array now has the magnetic material only on the top of the pillars. This process significantly improved the magnetic characteristics of BPM. A planarization by hydrogen silsesquioxane filling reduced the tribological interference of the protruding nanoisland heights in BPM.