This paper proposes a facile method to fabricate nanoporous microstructures by a photo-patternable SU-8 photoresist, to serve as a molecular filter in microfluidic systems. The fabrication process involves solvent-controlled nanoporous structure formation combined with standard photolithography steps for microstructure fabrication. The self-formed nanoporous morphology embedded inside the microstructure exhibits a sufficient mechanical strength and eliminates complex processes or protocols for integration/assembly of nano- and microstructures. Field emission gun scanning electronic microscopy (FEGSEM) images showed the fabricated nanoporous morphologies with embedded nanogaps of about 6-10 nm. Atomic force microscopy (AFM) images also depicted a clear difference on the degree of porosity between the solvent-controlled SU-8 and the standard resist. Fluorescent dyes, namely Rhodamine-B and Rhodamine-6G, were employed to estimate the diffusivity of the fabricated SU-8 based nanofilter and demonstrated that the Rhodamine based fluorescent molecules can penetrate these nanosized filtration structures. The fabricated nanofilter was capable of providing a molecular weight cut-off range up to 70 kDa, estimated roughly for a molecule with a diameter of 6-10 nm. This simple process provides a novel way to integrate the nanofiltration capability into microstructures while maintaining a sufficient mechanical strength for molecular level filtration in lab-on-chip (LOC) systems.