Atomic space is only empty of matter. Their are other things that call fill space. Among them are fields; electric and magnetic fields are common examples. In the case of atoms space is filled with electric fields. All atoms have tiny positively charged nuclei surrounded by relatively large regions of space that are filled with a negative electric field from the electrons in the orbit about the nucleus. When something else tries to pass through our empty space the negative electric fields interact and prevent it from passing through.
