The molecular-level chemistry involved in the processing of silicon and zirconia substrates by inductively coupled fluorocarbon (FC) plasmas produced from CF4 and C2F6 precursors has been explored. The roles of gas-phase excited, neutral, and ionic species, especially CF2 and F, were examined as they contribute to FC film formation and substrate etching. The surface reactivity of CF2 radicals in C2F6 plasmas has a dependence on substrate material and plasma system, as measured by our imaging of radicals interacting with surfaces (IRIS) technique. Relative concentrations of excited state species are also dependent upon substrate type. Moreover, differences in the nature and concentrations of gas-phase species in CF4 and C2F6 plasmas contribute to markedly different surface compositions for FC films deposited on substrates as revealed from x-ray photoelectron spectroscopic analysis. These data have led to the development of a scheme that illustrates the mechanisms of film formation and destruction in these FC/substrate systems with respect to CF2 and F gas-phase species and also Si and ZrO2 substrates.