The best we can do is calculate a very rough approximation.
Humans can see objects as small as 100 micrometres with the naked eye. A human egg cell, for example, is 130 micrometres in diameter, and its volume – assuming it’s a perfect sphere – is 1.15 million cubic micrometres. One of the most common molecules in the human body is glucose, containing 24 atoms: 12 of hydrogen, 6 of oxygen and 6 of carbon. Let’s pretend, for the purpose of this example, that a human egg is entirely composed of glucose molecules. The diameter of a glucose molecule is roughly one nanometre, and there are 1,000 nanometres in a micrometre.
So, for example, if you know that there are 1.15 billion glucose molecules in a human egg cell, and each molecule contains 24 atoms, that gives us 27.6 billion atoms in a single human egg cell, one of the smallest objects that can be seen by the naked eye. This is theoretical, of, course, but gives a good idea of the scale of atoms.