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The study of density of grain boundary defects and grain shape was conducted for Erbium doped Barium Titanate (BTE) thin films, which were deposited on Si(100) and Si(100)-Au substrates by electron beam physical vapor deposition (EB-PVD). The crystallite as well as grain size show strong dependence on thermal annealing. Analysis of surface morphologies revealed variations of growth, after thermal annealing process, in films deposited on Si(100) and Si(100)-Au. In films deposited on Si(100) and Si(100)-Au, the root mean square (RMS) roughness value increased from 1.95 to 6.33 nm and 1.73 to 12.9 nm, respectively. These values correspond to 3.2% and 3.7% of the deposited thickness, which is quite low in comparison to the film thickness. Diameters of cavities are observed more significant in films deposited on Si(100)-Au, which increased from 35 to 250 nm. Moreover, the evolution of growth also revealed changes in the surface morphology via surface energy analysis. The results also revealed that chemisorption and physisorption by grain boundary in Si(100)-Au substrate, makes the cavities hydrophilic. These observations are fundamentally important for understating the mechanism of formations of hydrophilic surfaces and changes in their properties owing to the interdiffusion and diffusion effects by the grain boundary. Furthermore, shape of the grains on the surface and the effects of density of grain boundary defects are discussed.