The microstructure of Y1Ba2Cu3Oy films and Y1Ba2Cu3Oy / Pr1Ba2Cu3Oy multilayers prepared by a pulsed organometallic beam epitaxy (POMBE) technique have been characterized by transmission electron microscopy (TEM). The microstructure of the films is observed to vary as a function of substrate temperature. At low temperatures, films are polycrystalline and exhibit some impurity phases. At higher substrate temperatures, films grow epitaxially with smooth surfaces and few impurities. Controlled growth at sufficiently high substrate temperatures allows uniform growth of alternating Y1Ba2Cu3Oy and Pr1Ba2Cu3Oy layers.