Contrary to popular belief, it is ultimately impossible to actually prove the existence of atoms due to the limitations of the senses. Even if one could see individual atoms by holding up and visually inspecting a given object, this would fail to do anything more than provide evidence for the existence of atoms, as seeing something does not mean that it exists outside of one's perceptions. It is thus irrational to believe anything more than that atoms are logically possible and that there is amassed scientific evidence, but not logical proof, that atoms exist [1].
The current conception of the atom presents it as a structure that breaks down into three basic subatomic particles, particles which are smaller than the atom itself. This means that atoms, according to the accepted model of today, are not fundamental (otherwise called elementary) particles. A fundamental particle cannot be broken down into underlying particles, like how an atom can be broken down into electrons, protons, and neutrons; a genuinely fundamental particle would be the end of an investigative road, as one could divide no further.
At the present time, only electrons are widely posited to be fundamental particles, as some scientists even make the (wholly unverifiable) claim that the quarks said to contribute to protons and neutrons ultimately reduce down to immaterial strings of energy, a notion referred to as string theory. However, it may come about that electrons are one day also said to reduce down to a smaller, more foundational class of particles. How could one actually demonstrate, and therefore know, that a particle is truly fundamental?
In short, even on a more "practical" level of empirical observation (as opposed to rationalistic inquiry), there is no way to guarantee that a particle is fundamental. Scientific ideas that seem to be correct are not guaranteed to reflect reality, after all. It would be a fallacious mistake to think that some new scientific discovery signifies the end of our ability to empirically explore a given subject simply because the discovery seems alien or revolutionary. Although historical evidence is of little value compared to logic, it is worth mentioning that atoms themselves were once reportedly considered fundamental particles, and now the opposite is widely considered true.
As long as there is a fixed starting point--for example, an object like a bowling ball has a specific finite shape and size--it is logically possible for a physical mass to be continually broken down into smaller material components. Size is relative, and there is no necessary point at which a particle could get no smaller. Instead of blindly asserting that science has yielded as much evidential information about the divisibility of subatomic particles as it can, a rationalistic approach to science acknowledges that any scientific discovery which is logically possible may one day be made.
[1]. https://thechristianrationalist.blogspot.com/2019/04/the-existence-of-atoms.html
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