i usually build a small shack around it. a little 2x2x2 with a roof on it is adequate.

for a portal to a swamp, i try to find a shoreline crypt, and i build on top of that and build stairs off the back side. Crypt entrance structure is invincible, and most things wont get up to the structure on top of it. and being on the shore, less chance of being jumped by enemies.