The bubbles are trapped air between the multiple layers of glass. While they are not a "Good Thing", they are not a big problem either. There is not much you can do to get rid of them at this point. A heavy flood of low viscosity epoxy followed by careful squeegeeing will reduce the problem in future boats. With a low viscosity resin the bubbles can rise to the surface.

Structurally the epoxy/fiberglass is not as strong as it could be, but not by enough that you will notice.

: I just finished glassing the exterior hull of my Guillemot 17, and was
: preparing to add a fill coat when I noticed thousands of tiny bubbles (at
: least I think they're bubbles) everywhere below the surface of the glass.
: They are all less than 1/64 inch across, and they are definately below the
: surface of the top layer of glass. They only occur where there are
: multiple layers of glass, and if you're standing more than three feet from
: the boat, you can't even see them.
: After having finished a Pygmy S&G boat earlier this year, I got a little
: cocky and thought I could lay up all three layers of glass on the hull at
: the same time as per the "standard" layup in Nick's book. I did
: a saturation coat on the entire hull the night before, and I applied the
: epoxy using a sqeegie and a brush, and pulled out the excess.

: I have three questions: first, how did this happen, and how can I avoid it in
: the future (other than applying one layer at a time). Next, is there a way
: to fix it? Finally, and most importantly, how will this affect the
: structural integrity of the boat?

: Any help is greatly appreciated!

: Todd