Atom is a word derived from ancient Greek. The philosophers Leucippus and Democritus had conceived of the universe as being constructed from tiny bits of hard matter, of differing shapes, that could not be broken into parts. Since the ancient Greek prefix for "not" is "a" and the word for "splittable" is "tomoi," these pre-Socratic natural philosophers called these tiny building blocks "atomoi." Modern scientists simply, adopted the word in describing the tiny bits of fundamental matter from which, they believed, all things were made.

Source:

Philip Wheelwright, ed., Tie Presocratics (Indianapolis, Ind.: Bobbs-Merrill, 1966).