This study presents a simple approach to perform selective mass transport through freestanding porous silicon (pSi) membranes. pSi membranes were fabricated by the electrochemical etching of silicon to produce membranes with controlled structure and pore sizes close to molecular dimensions (∼12 nm in diameter). While these membranes are capable of size-exclusion based separations, chemically specific filtration remains a great challenge especially in the biomedical field. Herein, we investigate the transport properties of chemically functionalized pSi membranes. The membranes were functionalized using silanes (heptadecafluoro-1,1,2,2-tetrahydrodecyl)dimethylchlorosilane (PFDS) and N-(triethoxysilylpropyl)-o-polyethylene oxide urethane (PEGS) to give membranes hydrophobic (PFDS) and hydrophilic (PEGS) properties. The transport of probe dyes tris(2,2′-bipyridyl)dichlororuthenium(ii) hexahydrate (Rubpy) and Rose Bengal (RB) through these functionalized membranes was examined to determine the effect surface functionalization has on the selectivity and separation ability of pSi membranes. This study provides the basis for further investigation into more sophisticated surface functionalization and coupled with the biocompatibility of pSi will lead to new advances in membrane based bio-separations.