The first issue is to identify what's causing the bubbles.

1) The most common problem is bubbles whipped into viscous epoxy (System Three is certainly viscous). The solution is to pre-warm both the hardener and resin and mix them carefully together (don't heat the epoxy after mixing because you are robbing yourself of precious work time (pot life)). The alternative is to use less viscous epoxy. The bubbles are trapped (as in cold honey) and may not have the time to get to the surface or pop before the epoxy thickens even further.

2) First pre-heat the wood with a hair dryer or increase the temperature in your shop. Turn heat down, wait 5-10 min and start applying epoxy. The cooling air in the wood will suck the resin into the pores rather than outgassing. If your shop is constant temp, this is not the cause. Also, this happens mostly when you seal the second side of the panel as opposed to the first coat on fresh unsealed plywood. The air is trapped and there is a higher chance for bubble formation.

3) Do yourself a favor and get rid off all the 'brushes' especially the foam types. Foam rollers and brushes are GUARANTEED to introduce froth into epoxy as you apply it over 'hairy and rough' wood grain. Use only plastic squeegee!

4) John has a good idea with the alcohol sprayed on the surface. Both alcohol and carbon dioxide (in a torch) reduce the surface tension of the epoxy allowing the small bubbles to escape. Heating the epoxy after application is however going to cause outgassing.

My suspicion (without knowing more details) is that your shop may be a bit too cold and the epoxy too viscous.

Vaclav