Erkin,

Your best bet would be to overfill the entire area (so the pillars are
under "water" so to speak), then etch back with a plasma. If using a
photoresist, don't pattern it at all. Just post-bake it or hard bake.

Only other way I can think of (w/o CMP) is to overfill with some really
soft material like a wax and then razor-blade the surface at your specific
height. There are some setups commercially available for casting thin
layers that use a suspended razor blade to fix the film thickness (by
passing back and forth over the film as it dries). You might be able to
get away with hand sanding or polishing a soft fill material also.

Mike