Once you've crafted certain items (like Base pieces, Vehicle Garage, etc) and clicked the Place button, you will be taken to a top-down, 3rd person view where you can place the object in the world.
You can move around as usual (WASD) in this top-down view and a translucent representation of the object will indicate where the new object will appear if you build it. If the object is red, that means you can't build it in that exact spot as it would be colliding with another, existing object. If it is not red, then that means you can place the object there. Left-click an open spot to place the piece.
NOTE: Although it's possible to place Base pieces anywhere on the map, you'll most often want the Base pieces to connect to the rest of your Base. To do so, make sure the portal of the new Base piece is lined up with the portal of an existing Base piece before you place the new one. If it isn't lined up, press R to rotate the piece until it is.
NOTE: When placing objects, you can move around in the top-down view, but the player still has collision and it can be easy to get hung up inside of your Base. An easier method is to switch to first-person by pressing C and then walking to where you want to place your new object.
Once you've clicked to place the object, nanobots will build it and you will be able to enter your new base piece, use your garage, or whatever.
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