Epitaxial rare earth manganite thin films (ReMnO(3); Re = Tb, Ho, Er, and Y) and multilayers were grown by liquid injection metal organic chemical vapor deposition (MOCVD) on YSZ(111) and the same systems were grown c-oriented on Pt(111) buffered Si substrates. They have been structurally investigated by electron diffraction (ED) and high resolution transmission electron microscopy (HRTEM). Nanodomains of secondary orientation are observed in the hexagonal YMnO(3) films. They are related to a YSZ(111) and Pt(111) misorientation. The epitaxial film thickness has an influence on the defect formation. TbO(2) and Er(2)O(3) inclusions are observed in the TbMnO(3) and ErMnO(3) films respectively. The structure and orientation of these inclusions are correlated to the resembling symmetry and structure of film and substrate. The type of defect formed in the YMnO(3)/HoMnO(3) and YMnO(3)/ErMnO(3) multilayers is also influenced by the type of substrate they are grown on. In our work, atomic growth models for the interface between the film/substrate are proposed and verified by comparison with observed and computer simulated images.