Of course it is difficult, if not impossible, to know whether classical philosophers that talked about atomism thought that "atoms" could be manipulated by men. However, I was startled to know that even at the beginning the 20th century, there were scientists who disputed the existence of atoms, and that it took the explanation of Brownian effect by Einstein to convince them.
My understanding - but I may be wrong - is that the early chemists at the end of the 18th century talked about substances, non atoms: some chemical compounds were considered basic. So, when did atomism started to gain widespread, even if not global, acceptance?