Here's the thing though, doctors have a long storied background of not knowing what the hell they're doing. History is filled with stories of hilarious medical ineptitude, and in all likeliness, today's medical practices will be similarly snorted at 100 years down the road.
Empty definition, containing nothing; having none of the usual or appropriate contents: an empty bottle. See more.
It appears to be the standard thing to say that 'atoms are mostly empty space'. This implies that the constituents of the atom, the electrons and nucleus (quarks at the most fundamental level) are something other than empty space, like little bits of matter, that they take up space.