Physical and chemical changes in a polished wafer and in $2.5{mu}m$ & $4{mu}m$ epitaxially grown Si layer wafers (Epilayer wafer) after surface treatment were investigated. We characterized the influence of surface treatment on wafer properties such as surface roughness and the chemical composition and bonds. After each surface treatment, the physical change of the wafer surface was evaluated by atomic force microscopy to confirm the surface morphology and roughness. In addition, chemical changes in the wafer surface were studied by X-ray photoemission spectroscopy measurement. Changes in the chemical composition were confirmed before and after the surface treatment. By combined analysis of the physical and chemical changes, we found that diluted hydrofluoric acid treatment is more effective than buffered oxide etching for $SiO_2$ removal in both polished and Epi-Layer wafers; however, the etch rate and the surface roughness in the given treatment are different among the polished $2.5{mu}m$ and $4{mu}m$ Epi-layer wafers in spite of the identical bulk structural properties of these wafers. This study therefore suggests that independent surface treatment optimization is required for each wafer type, $2.5{mu}m$ and $4{mu}m$, due to the meaningful differences in the initial surface chemical and physical properties.