Is your skimmer hang on tank?
What kind of skimmer is it?
If it is in the sump, do you have a bubble trap?
My sump has no bubble trap, and the skimmer is at the wrong end (should be the first thing in your sump IMO)...even so, outflow, and return pump in flow are in opposite directions and I have NO micro bubbles.
Somethings you can do:
Buy a bubble trap built for your skimmer.
Put something over the return pump intake, or the skimmer outflow to trap bubbles (sponge etc)
This is an easy fix, just give us some more details.