Atomic diameter-scale measurements

To be more precise: can we put two objects together so there will be a space with width of one (or some number below 10) atom's diameter(s) between them?

For the question to make sense, you would need the surface of each object to be perfect, following a flat crystal plane. Then, because of quantum mechanics, an atom doesn't have a defined size. By the time the two surfaces would at about the atom-atom distance in the crystal, they would already be consider to be touching each other.

Well, kind of yes.

Images can be made so measurements can be taken, but with this size it's already no longer simple what will an image show or what will a measurement measure.