A Planck length is 1.6 x 10^-35 meters (a zero then a decimal point, then 34 zeroes then a 16). This represents the shortest measurable length, beyond which the universe is theoretically probabilistic and indeterminate.
A hydrogen atom comprises one proton and one electron. The electron is a massless point particle and the proton is one 100,000th the size of the atom, meaning 99.999% of the atom is ‘empty space’.
The average density of matter (including dark matter which has never been detected) across the entire universe is the equivalent of 6 hydrogen atoms per cubic meter or 0.0000000000000000000000000000004%.
We can only tell that things exist when they interact - when they deflect one another. To detect the sub-atomic world, the 27 km Large Hadron Collider has to fire two high-energy particle beams at each other at close to the speed of light.
The atomists of the 5th century BCE believed everything was composed of "atoms". These they described as physically indivisible, that is, they were the smallest things possible, and between them there was empty space.