Which shields do you mean? The first ones (you can disable them via some levers in the fortress; you enter the fortress via a teleporter) or the second ones (at the goblin-settlement)?
For the first shields, ignore the nests, port into the fortress, kill the people there, use the levers, then blow the nests away; for the second shields (not around the harbour, you cannot disable those) just kill everything you can reach, blow of the buildings with the blue glow and then kill that flying mega-goblin and the shields will also go down.