Not by actually viewing them directly. No totally indirectly by means of elements and compounds and rules of proportions. Later brownian motion seemed further indirectly give evidence for atoms. Only today do we have STM's and AFM's to directly detect atoms, but even they do it indirectly by getting data and using advanced mathematics that would convert it into geometry. Only indirectly did Einstien figure out that gravity is curviture of some barelly defined spacetime term, and that was by means of a system of reference frames which barelly has anything to do with curviture of some still undiscovered quantum field.
Every theory incompletelly describes nature.