Fluorocarbon-based chemistries were used to study the effect of wafer temperature on the etch of high aspect ratio hardmasks composed of SiO2 and SiNx layers. It is found that etch stop can occur easily at high temperature. The rate of polymer deposition plays an important role in etch stop. The etching rates were found to be inversely proportional to the wafer temperature. Such a relation indicates a negative activation energy in the rate expression of hardmask etching using fluorocarbon plasma. It also implies that in hardmask etching, complicated gas-surface, but not simple one-step, reactions are involved. Different wafer surface temperature can provide different degree of activation for etching reactions. Analysis of etching rate and optical emission trends indicates that CFx may contribute more than F does in the etch of SiO2 and SiNx, since polymer-rich etching chemistries were used. Based on the temperature-dependent etching rate, we propose a reaction mechanism for the reaction trends observed in hardmask etching.