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This paper investigated a number of environmentally friendly fluorocarbon and hydrofluorocarbon (HFC) gas chemistries for sidewall passivation during time-multiplexed plasma etch processes of through-silicon vias (TSVs). The effect of plasma processing conditions on TSV etch rate, etch selectivity, and mask undercut was examined. The choice of passivating gas on TSV sidewall roughness was studied using atomic force microscopy (AFM). In addition, blanket fluorocarbon films were deposited, etched, and characterized with x-ray photoelectron spectroscopy (XPS) to study the effect of film chemistry on polymer growth and etch rates. We observed that sidewall film deposition rate, sidewall film etch rate, and degree of crosslinking in the passivating film tended to predict results of mask undercut and selectivity. Compared to octafluorocyclobutane (C4F8) processes, recipes using the four test gases generally showed a reduction in mask undercut, an increase in selectivity, and a decrease in sidewall roughness at the cost of reduced silicon etch rate.