Coming to an observation

How did human went from day-to-day objects to knowing the size of an atom. In reality, without any particular equipment, imagining that the hair of your body constitutes of millions of atoms along its diameter. What is the thought process and actions leading to measuring the size of an atom…, my eyes find it hard to pierce into an hair strand and augment realize the atom in it… I have to believe in reality, and reality of atoms is quite brain consuming, especially, when putting a scale measuring millions on a an body hair, thats way too many objects to keep track of ..!!!

If I had to transport atoms in the body accurately, what kind of organism would I need to be?, what kind of machine would I need ? magically one may edit their body atom-by-atom, while keeping the conscious form alive..