The effects of deuteration and helium-implantation on the surface morphology and phase structure of scandium (Sc) thick film are investigated by X-ray diffraction (XRD), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM) methods. The preferred orientation of (002) crystal plane is observed for both films deposited on substrates of monocrystalline-silicon and polished-molybdenum. A great number of holes appear on surface after deuteration and the grain size of ScD2 is bigger than that of Sc, whereas a few ScD0.33/Sc grains with relatively small grain size retain inside crystal. The surface morphologies of scandium and scandium deuteride films are slightly affected by helium-implantation. The formation of helium bubbles with a preferred orientation in the crystal lattice of scandium and scandium deuteride, generated by the aggregation of ion-implanted helium, causes the corresponding diffraction peaks of scandium and scandium deuteride phase to shift towards smaller angles.