Reflow Soldering QFNs with Thermal Vias and Filled Vias in EAGLE
Print the solder paste over the thermal pad only and reflow (or tin it with a regular solder using larger iron), let cool, apply the paste over the board, populate and reflow.

On the next revision make thermal vias smaller. I tend to pick next to the smallest allowed drill size.

Some boardhouses do filled vias if you specify it along with a compatible finish, i.e.HASL.