The surface quality of a mold is one of the major factors in imprint lithography as it determines the final surface quality and the minimum size of the replicated patterns. This paper describes a process for O₂-based reactive ion etching (RIE) of glassy carbon (GC) without encountering any micro masking effect. Glassy carbon, because of its attractive properties such as its surface inertness, thermal stability and extraordinary hardness, has drawn much interest as a mold material for high-temperature imprinting on glasses and metals. Etch profiles with highly smooth surfaces free of micro masking effects were achieved by adding SF₆ to the etching gas. The fraction of SF₆ in the gas mixture (ranging from 0.1 to 0.6) showed little change in the quality of the etched surface, but it did lead to a proportional decrease in the etch rate of GC. A reasonable GC etch rate (115–120 nm min⁻¹) and a smooth etch surface were obtained using SF₆ at a fraction 0.2 or below. Using electron beam lithography (EBL), and processing under the established SF₆/O₂ RIE conditions, GC molds were fabricated and successfully applied to thermal imprinting onto glass and metals.