Amorphous hydrogenated carbon (a-C:H) films prepared by plasma polymerization can contain chemical species due not only to the process gas species, but species from prior processes in the deposition chamber. Our studies showed that standard O2 etching/cleaning processes done prior to plasma film formation will affect future film deposition rate measurements and carbonyl group formation. Additionally, substrate etching by polymer forming gas species is shown through the 956 cm-1 negative peak in the IR spectrum.