Automotive filler works just fine, but I would recommend first sealing the MDF with Sanding Sealer before putting the auto filler on. The sanding sealer I use is oil-based, not acrylic.
The sanding sealer strengthens the edges of the MDF and stops the telephone-book delaminating that MDF is prone to. You can sand a much sharper edge this way. Then you can use the auto filler to build up low spots, etc.