There are things or entities in or on an object that could be present and be proven to exist by experiments and yet one can not see because they are too small to be seen by our naked eyes or some cannot be seen at all. Examples are viruses, bacteria, molecules, ions, atoms, forces, forms of energy, etc.

People of long ago, at around 5^th century B.C., a Greek Philosopher named Leucippus thought that water has an ultimate particle that cannot be subdivided. His idea was later expanded by his student, Democritus who named these possible indivisible particles as “atomos”. From there, scientists tried to experiment in order to verify its existence and farther they go into figuring out how ”atomos” looks like.

John Dalton theorized that an atom is a solid sphere which we can call “billiard ball model”; J.J. Thomson theorized that atom is like a “raisin pudding” where the pudding is a pool of positive particles and the raisins are the negative particles. We can call this the “watermelonmodel”, if you cut a watermelon in halves, the randomly distributed seeds represent the negative particles like that of the raisins in the pudding;  Ernest Rutherford with his experiment on thin gold foil struck with alpha particles, figured out that atom is like that of the planetary system, where  a massive part at the center(analogous to the sun) and some particles are revolving around it(analogous to the planets). We can call this model as “microplanetary system”.

Scientists did not stop there, they continue to experiment and to theorize the existence and structure of atom. In adaptation of Max Planck’s idea that energies are quantized (in specific regions), Neils Bohr theorized that the particles (electrons) around the center (nucleus) of the atom are in circular orbit about a particular distance from the nucleus, in an allowed energy state. Louise de Broglie and Erwin Schrodinger of course did not fully agree with Bohr, so they  studied, contributed and arrived to  the quantum mechanical model or the electron cloud model of atom. They based their model on Werner Heisenberg Uncertainty Principle. 

According to Heisenberg, it is  impossible to know simultaneously both the exact location and momentum of an electron. Thus, there is no way that Bohr can tell with certainty at what particular distance the electron is from the nucleus. According to Schrodinger we can only talk of the probability (possibility) of finding an electron at a certain region in space, we can not pinpoint its location exactly.

Years by and by, At last! Atoms can now be seen. Thanks to the invention of Scanning Tunneling Electron Microscope. This electron microscope has at least proven that an atom is spherical in shape. Congratulations to  Dalton, he really had done a great job in figuring out the shape of an atom.