The self-spreading behavior of DMPC bilayer containing TR-DHPE molecule was observed in the presence of channel-type nano-architecture (nano-channel). The concentration of TR-DHPE at the spreading edge region was gradually decreased by passing through the nano-channel. The filtering efficiency was increased by elongating the channel-length, which was explained by considering a formation of a local compressed state of the spreading bilayer in the elongated channel region. In addition to the channel length, the filtering effect was found to be tuned by the channel angle (entrance angle). These two dependencies are important for precise control of filtering efficiency and selectivity.