The synthesis of mesoporous silica thin films using surfactant templating typically leads to an inaccessible pore orientation, making these films not suitable for membrane applications. Recent advances in thin film synthesis provide for the alignment of hexagonal pores in a direction orthogonal to the surface when templated on chemically neutral surfaces. In this work, orthogonal thin film silica membranes are synthesized on alumina supports using block copolymer poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (P123) as the template. The orthogonal pore structure is achieved by sandwiching membranes between two chemically neutral surfaces, resulting in 90 nm thick films. Solvent flux of ethanol through the membrane demonstrates pore accessibility and suggests a silica pore size of approximately 10 nm. The permeability of ions and fluorescently tagged solutes (ranging from 4,000 to 70,000 Da) is used to demonstrate the membrane’s size selectivity characteristics. A size cut off occurs at 69,000 Da for the model protein BSA. By functionalizing the silica surface with a long chained alkyl group using n-decyltriethoxysilane (D-TEOS), the transport properties of the membranes can be altered. Contact angle measurements and FTIR results show the surface to be very hydrophobic after functionalization. Solvent flux of ethanol through the silica thin film membrane is similar before and after functionalization, but water flux decreases. Thin film silica membranes show much promise for applications in catalysis, bio-sensing, and affinity separations.