Plasma polymerization is a common technique used for the deposition of thin polymer films. Radio frequency (rf) sputtering may also be employed for plasma polymerization with the principal difference being the introduction of fragmented polymer species (for the latter) rather than gaseous monomer species into the plasma. The thrust of this work is to study the integrity of thin films prepared by rf plasma sputtering of two substantially different polymer systems. Polytetrafluoroethylene (PTFE) has a simple linear chain molecular structure and is noted for its lubrication and nonwetting properties. Conversely, polyetherimide (PEI) possesses a complex ring molecular structure and is known for its dielectric strength and high temperature stability. The techniques utilized to characterize the films were x-ray photoelectron spectroscopy (XPS), DRIFT, UV-Visible, x-ray diffraction, and scanning electron microscopy (SEM). Periodic controlled ion sputter treatment during XPS analysis of both virgin and sputtered deposited films was also found to be a method of inducing simulations of some of the effects of sputter-deposited growth. Thin films prepared from targets of both polymers were found to be amorphous. DRIFT observations showed a dismantling of the PEI molecule with a total elimination of C=O and C-O groups, and fracturing of the imide group. The retention of some benzene groups, with a partial aromatic to aliphatic transition was also observed. These results were supported by XPS-findings. Conversely, PTFE films were found to contain CH, CF, CF2, and CF3 structural units like those found in plasma polymerized PTFE films. After nominal sputter treatment, the CH, CF2, and CF3 species were significantly removed while the CF content appeared to increase, indicative of damage from ion beam exposure. For PEI films, further rearrangement of the C(ls), O(ls), and N(ls) peak structures occurs from ion beam exposure resulting in the formation of C and N variants. While PTFE films are similar to their parent material, observations of rf sputtered PEI indicate a very different type of film formation.