Industries such as textile, paper, plastics etc. release dyes to wastewater and even the presence of very small quantities of dyes (less than 1 ppm) is noticeable and unacceptable. Nanotechnology have discovered new filtering Nanofibrous membranes offer unique properties for filtration- and adsorption-based separation including high specific surface area, good interconnectivity of pores and potential to incorporate active chemistry on a nanoscale media for effective filtration. The nanofiber based filtering media, made up fibers of diameter ranging from 100 to 1000 nm, can be conveniently produced by electrospinning technique. In this investigation nanofibrous mambranes have been produced from three kinds of polymers polyacrylonitril, polyester and functionalized polyester with same thickness(40µm) and average diameter of nanofibers(308-317 nm). The maximum efficiency of these 3 membranes was achieved with membrane based on functionalized polyester nanofibers. So membranes based on functionalized Polyester nanofibers have been selected for surveying the effects of filtration and electrospinning process parameters. In this work, C.I Basic Blue 3 dye used. In surveying the filtration process parameters, the dye removal decreased with the applied pressure and feed concentration. With increasing the filtration time, dye removal has been significantly increased up to 60 min but after that the dye removal increased slowly with time. Also two kinds of cross-flow and dead-end filtration system design have been tested which dead-end system had higher removal percentage. In surveying the electrospinning process parameters the dye removal decreased with concentration of polymer in solution and increased with applied voltage. Dye removal also increased with time of electrospinning up to 3 hours but after that decreased with electrospinning time. Dye removal of 98.6% was obtained from electrospinning of 20% w/v functionalized polyester in TFA/DCM 70:30 solvent mixtures conducted at 20kV applied voltage with flow rate of 0.26 ml/h for 3 hours on a carbon foam base and using this membrane in a dead-end circulated system for feed concentration of 0.019 gr/lit dye at pressure of 1.25 bar for one hour. Interior pore blocking filtration mechanism for nanofibrous functionalized polyester membrane and cake formation mechanism for nanofibrous polyacrylonitril and polyester membrane were determined. It can be said that in removal of C.I Basic Blue 3 from wastewater by nanofibrous functionalizd polyester membrane, in addition to physical sieving the dye molecules, the electrostatic interactions between dye molecules and pore walls plays a significant role.