Millimeter sized arrays of uniformly-distributed nanopores (180-220 nm) were created in thin (200 nm) silicon nitride membranes using interferometric lithography. Molecular transport properties of the fabricated devices were investigated experimentally and compared with those of state-of-the-art polycarbonate track etched membranes. Two similarly-sized proteins, bovine serum albumin (BSA) and bovine hemoglobin (BHb), were used as permeates in the transport experiments. Up to 40 fold higher pore fluxes were achieved with unmodified silicon nitride membranes relative to thicker commercial nanoporous membranes. Similarly, in mixed protein experiments, ∼5.0 and 1.9 fold higher BSA and BHb selectivities were obtained with fabricated thin membranes at pH 4.7 and 7.0, respectively, relative to the commercial nanoporous membranes.