Two-dimensionally standing graphene sheets, i.e., carbon nanowalls (CNWs), were synthesized on a Si substrate employing a capacitively coupled fluorocarbon plasma-enhanced chemical vapor deposition system together with H radical injection. To apply CNWs in electronic devices and/or membrane filters, we have demonstrated the reactive ion etching (RIE) of CNWs. RIE employing H2/N2 gases showed that the CNW films were anisotropically etched at a relatively high rate of more than 250 nm/min. However, the 10-nm-thick interface layer between a CNW film and the Si substrate remained and the interface layer was not completely etched. In contrast, RIE employing Ar/H2 gases enabled us to completely remove the interface layer. Ar/H2 RIE was also carried out from the bottom surface of CNW films after exfoliating them from the Si substrate. As a result, a free-standing CNW film of 550 nm thickness without an interface layer as a membrane filter was successfully formed.