Natural portals are generated as part of the terrain. They are immovable and can not be controlled by the player. The destination of each portal is predetermined in the world generation phase.
Natural portals are most common in a temple-like structure, with a slot directly above the portal sometimes containing a ruby. Putting a ruby in this slot activates the portal, and walking into the portal after doing so teleports you to the predetermined destination of the portal.
Natural portals can also spawn in clusters inside of tentacle rocks (I don't know if that's the correct terminology). Inside these rocks, portals are surrounded by corrupted stone with multiple rubies nearby each one. These can be activated by placing a ruby somewhere slightly above the corrupted stone structure that holds the portal.