Ultrathin silicon nanoporous membranes with multiple pores were fabricated using batch processes involving chemical vapor deposition and rapid thermal annealing. Transmission electron microscope images showed the existence of nanopores with an average pore size of 13 nm. Measurement of ionic conduction of electrolytes with varying conductivity across the membranes confirmed the existence of pores and the repeatability of the process. The functional diameter of the pores was determined by analyzing the permeability of several industrially and medically important globular biomolecules of varying sizes such as α-amylase, bovine serum albumin, catalase and xanthine oxidase. Biomolecules with hydrodynamic diameters up to 8 nm passed through the nanopores, whereas the passage of the larger molecules was hindered. The surface charges on the molecules determine the functional diameter of the pores, and hence the permeability, as substantiated by varying the pH of the buffer solution. The filtered proteins were found to be uncleaved from sodium dodecyl sulfate polyacrylamide gel electrophoresis, and the enzyme assay of the filtered amylase showed that the activity remained unchanged. © 2002-2012 IEEE.