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The microstructures of the Bi0.4Ca0.6MnO3 (BCMO) and La0.67Ca0.33MnO3 (LCMO) epitaxial films are investigated by transmission electron microscopy in detail. BCMO epitaxial films (~ 10 and ~ 40 nm) exhibit an island growth mode whereas the LCMO films (~ 6 and ~ 30 nm) follow a layer by layer growth mode. Combined with the critical thickness models for the expected onset of the misfit dislocations in epitaxial films, an atomic collapse model is introduced to explain their mechanism of formation in manganite films. At the beginning of deposition, the strain caused by the lattice mismatch between the epitaxial film and substrate can be accommodated by elastic deformation. With the increase of film thickness, the strain becomes larger and larger. When the film thickness reaches the critical thickness, the strain can only be relaxed by the formation of misfit dislocations. Meanwhile, the atomic configuration of the epitaxial film will reorganize and some atoms begin to collapse, thus an island morphology will be formed. Once the collapse morphology is formed, maintenance of this wave-like morphology depends on atomic diffusion length of the deposited atoms. If the diffusion length of the deposited atoms is long, the island morphology will not be maintained. If the diffusion length of the deposited atoms is short, the island morphology will keep until the epitaxial film is thick enough. The results could shed light on the growth modes for other perovskite epitaxial films.