A moat works to keep out some enemies, and could even be stretched out far enough to prevent ranged attacks, but a raised ground wall will keep out everything -as long as it's tall enough. Forget spikes, and fences. Both of which are badly implemented.

Make a cart, and grind as much stone as you can. If your base is large in size, make sure your work table spam is spread out far enough to encompass your entire base. To make certain enemies cannot spawn inside your base.

You can do things to remove spawn points, but if you take them away, the enemy will spawn again.