Step one: find a build location devoid of enemies (if enemies are spawning in your base it is because you base is built upon their spawn)
Step two: build

Only solution is to bring in the part of your base where they spawn. Otherwise it will just keep happening

~ I set up on a sandy bar that is sandwiched between 3 greydwarf spawns, one troll spawn, 3 neck spawns, a deer spawn. I built a third story lookout so I can see what needs to die at dawn