We present a novel microfilter system used for the selective separation of solutes of molecular sizes 1–2 nm. The microfilter system consists of two layers of micro chambers made of PDMS and one piece of porous membrane made of polyethersulfone (PES) using the wet-phase inversion method. The PES membrane at the center of the two micro chambers acts as a barrier to molecules larger than its pores. A novel method of bonding the PES membrane to PDMS surface was developed in the device fabrication, whereby diffusion in the microfilter was theoretically derived and applied in the filtering evaluation. The filtering capacity of this microfilter for molecules of molecular sizes from 0.3 nm to 6.6 nm was evaluated using solution samples of sodium chloride (NaCl) and fluorescein isothiocyanate (FITC) dextrans with molecular weights of 4k, 20k and 70k, respectively. The filtering experiments indicated that the optimal membrane used for the device was P2S2. This microfilter system with optimal PES membrane was believed to be capable of selective separation at a molecular size barrier of 1–2 nm and also believed to have the potential for use in portable hemodialysis systems.