The current model of the atom was empirically developed without ever really viewing atoms because the individual components of atoms each have different, unique physical properties.
Next, Joesph Thomson discovers electrons in 1897 while working with cathodes, which were attracted to positively charged electrical plates and thus were of negative charge. He then theorized that atoms were in fact divisible, and that the atom was a positively charged sphere with little “corpuscles” of negative charged distributed evenly throughout.
Then in 1909, Ernest Rutherford discovers the proton in an experiment involving alpha particles being ejected at a very thin sheet of gold foil. A very small number of particles were reflected back, contrary to the expected result that they would pass right through since “the atom was of a uniform charge throughout”. Him and his colleagues discovered that atoms were almost entirely empty space with a positively charged, very concentrated nucleus that electrons orbit.
Finally, James Chadwick discovered the neutron to account for mass that physicists couldn’t otherwise describe, which was the third and final component of the subatomic particles that make up atoms. However, other physicists and mathematicians later discovered that the universe at the atomic size is very probabilistic, and that the true location of electrons cannot really be known, thus giving us our current, electron cloud model of the atom.