>>13270895Atoms are the smallest units of matter that we can work with at the moment when it comes to engineering stuff. If you want to change the composition of atoms in some way, then use chemistry.
Inserting something "through" atoms themselves would only break these atoms apart. If the atoms you are working with are something besides Thorium, Uranium, or Plutonium, the amount of energy required to split the atom in the first place would be too much to be of any practical use when it comes to machining things.
tl;dr atoms are the smallest units we can work with when it comes to materials. If you want to change the composition of atoms, use chemistry. Boring through atoms themselves would require too much energy to be practical.