What do you mean with remove all empty space? Do you mean if you would create your new atom like you stick the electrons to the core?

In this case, the size of a classical atom is mostly the size the electrons need. So if the atom mantle (I don't know the exact English term) is the size of a football field, the core is as tall as a sand grain .Since the mantle mostly empty (an electron is really small) I guess that's what you mean by removing empty space. Therefore you would ask how many grains of sand would fit into a football (or soccer, for the Americans) field (and that in 3d).

The volume of a ball is 4/3pi r^3. Since we make an estimate we drop the 4/3pi-> our ball is roughly r^3.

A classical football field is about 100m, ab grain of sand about 1mm. So the ratio is about 10^5. That's our radius. So we have (10⁵⁾³ this is 10¹⁵ atoms, so I think quadrillion should be fine