In this paper, we report the fabrication of carbonaceous nanofiber (CNF) membranes functionalized by beta-cyclodextrins (CNF-β-CD membrane) and their application for molecular filtration. The chemically synthesized carbonaceous nanofibers were first functionalized by β-CD, and the free-standing CNF membrane can be prepared by a simple filtration process. The membrane shows a remarkable capability to function as an ideal molecular filter through complexation of phenolphthalein molecules with the cyclodextrin molecules grafted on the CNFs. As a typical dye pollutant, fuchsin acid can also be effectively removed from the solution through such a membrane. Engineering the surface of this carbonaceous nanofiber membrane may allow it to be used for other applications such as chiral separation and drug delivery.