Poly(ethylene terephthalate) and poly(imide) surfaces pre-treated by $O_2$ plasma were modified by two-step $CHF_3$ plasma, and the plasma modified film surface were investigated with scanning probe microscopy, X-ray photoelectron spectroscopy, and contact-angle and surface energy to characterize the surfaces. The surface energies were calculated from measured contact angles between several solutions and film-based on geometric means and the Lewis acid-base method. The exposure of the PET and PI film surfaces pre-treated by $O_2$ plasma to the two-step $CHF_3$ plasma led to the decrease in surface roughness and increase of the contact angles of film in water and surfactant solution. Primarily because of the contribution of polar force, the surface energy and hydrophilicity of PET and PI film treated by $CHF_3$ plasma decreased greatly. Electron spectroscopy for chemical analysis (ESCA) indicated that the $CHF_3$ plasma treatment introduced fluorine functional groups led to a decrease of the surface energy and hydrophilicity of PET and PI film.