How do you isolate just a single atom of an element in artificial vacuum?

There are many possible answers to this question - I will offer one approach that we use in our lab to trap individual Rubidium atoms.

The key idea is that of the 'optical tweezer', which is a tightly focused laser that is off-resonant from an atomic transition. Since the laser is off-resonance, it does not scatter very many photons from atoms, but instead it forms a potential well in which atoms can be trapped. If the focused laser is not too tightly focused, then it can trap a large number of atoms. If it is very tightly focused (ie., a waist of around a micron), then the tweezer is in the 'collisional blockade' regime. In this case, shining a near-resonant laser (often used for laser cooling) will cause two trapped atoms to collide and be lost from the trap.

In this case, pairs of atoms are ejected from the trap. But if a single atom is left in the trap, it will happily remain there by itself. Tweezers in this configuration can therefore trap at most a single atom, which can be detected by fluorescence imaging. People have used this technique to create large arrays of individual neutral atoms, which then can be used for a variety of experiments in quantum physics.