I don't understand the question - do you have some sort of Render Elements set up, that show only particular objects? If so, what kind, and what is the intention of using them? The Beauty pass should have everything in it, and you could just save that. If you do have Render Elements set up, Save All will save them all to something like an EXR, or to separate images for things like PNG and JPG, so then you should still end up with the result 3 that you can see in the frame buffer.