Thin film CdTe solar cells have been recognized as reliable alternative for the manufacturing of cost efficient photovoltaic solar cells of the future, due to its excellent absorber characteristics and simple, low-cost manufacturability. However, for the attainment of higher cell performances, additional studies are needed to increase cell efficiency through further development of better quality films and new fabrication processes. In substrate-structured CdTe thin film solar cells, the CdTe absorber is deposited directly onto the substrate or through a back contact layer. But the quality of deposited film is believed to depend on the type and smoothness of the substrate. In this work CdTe was deposited on different substrates by RF sputtering and the effects on the deposited films were studied in terms of their structural and morphological forms. The substrates used are pure molybdenum sheets (Mo), molybdenum-sputtered molybdenum (Mo/Mo), molybdenum-sputtered polyimide (PI/Mo) and molybdenum-sputtered glass (glass/Mo). The characterization tools used include XRD, SEM and AFM. The results show that all surfaces produced uniform, compact and pinhole free films; however, those on smoother surfaces produced larger as-deposited grain sizes of up to 1.7μm as against 1.3 for rougher surfaces. Non-uniformities such as overgrowth and voids were observed, but only films on PI showed evidence of cracking and peel-offs.