My game, for example, has multiple "rooms" that collectively make one entire level or area, like in Metroid. Each "room outline" or "camera zone" is loaded at the beginning of the layout. Then, whenever my player enters a new room, the entire level is loaded and everything outside of the current room is destroyed.
So yeah. Basically it loads small parts of the level one by one, and destroys what is in other rooms, clearing up thousands of objects.
That's one way to do it atleast..Dunno what to tell you if your world is just one giant open area. Maybe try breaking it up into multiple layouts?