Nanoporous membranes are applicable to a variety of research fields due to their ability to selectively separate molecules with high efficiency. Of particular interest are methods for controlling membrane selectivity through externally applied stimuli and integrating such membrane structures within multiscale systems. Membranes comprised of deterministically grown, vertically aligned carbon nanofibers (VACNFs) are compatible with these needs. VACNF membranes can regulate molecular transport by physically selecting species as they pass between the fibers. Defined interfiber spacing allows for nanoscale control of membrane pore structure and resultant size selectivity. Subsequent physical or chemical modification of VACNF structures enables the tuning of physical pore size and chemical specificity allowing further control of membrane permeability. In this work, the dynamic physical modulation of membrane permeability that results when VACNFs are coated with an electrically actuatable polymer, polypyrrole, is demonstrated. Electrochemical reduction of polypyrrole on the VACNFs results in controlled swelling of the diameter of the nanofibers that in turn decreases the pore size. Dynamic control of membrane pore size enables selective transport and gating of nanoscale pores.