An atom is the smallest unit of ordinary matter that forms a chemical element. It is fundamental to the structure of the world around us. However, the origin of the word "atom" is not related to either its size or its role in the structure of the universe.

The English language contains many words of Greek origin such as “amoral” or “atheist” where the “a-“ at the beginning means “not.” So, for example, “asymmetric” is “not symmetric”. The origin of the word “atom” is similar. The “-tom” part comes from a Greek word meaning “cut” or “divide.” So, the original word “atomon” (ἄτομον) signifies “that which cannot be cut” or "that which cannot be divided."

But the irony, of course, is that the word “atom” has proved to be inappropriate. From scientific discovery in recent centuries we now know that the entities we still call atoms can indeed be divided and that they are made from more fundamental particles.

More Info: en.wikipedia.org