We have investigated the transport properties of track-etched poly(ethylene terephthalate) (PET) membranes in order to pursue possible applications for effective separation and sensing purposes. We have obtained cylindrical and conical nanopores on PET membranes using symmetrical and asymmetrical track-etch methods, respectively. We have used the fabricated nanopores for the transport of charged dye molecules. Effect of applied potential, temperature and pore geometry was shown for crystal violet dye. We have also investigated the transport of methyl orange and shown negatively charged carboxylate groups on the PET nanopore walls along with applied potential enhanced the selective transport of cations. The temperature and the conical geometry were also found to promote the transport of cations.