I am not familiar with the Skutt kiln, but there is a lot of information on the internet about doing a "bubble squeeze". Essentially, you are holding the glass at about 1000 degrees for an extended period of time to let the glass settle and the bubbles escape. Google and you should find plenty of info.
If your Skutt program does not incorporate a squeeze, you may want to look at creating a custom firing program.
You can also design your pieces so that the chance of trapping bubbles is minimized, but that is essentially a top layer that is comprised of multiple pieces (which doesn't sound like it would work in your case).