Porous thin films containing subnanometer channels oriented normal to the surface exhibit unique transport and separation properties and can serve as selective membranes for separation and protective coatings. While molecularly defined nanoporous inorganic and organic materials abound, generating flexible nanoporous thin films with highly aligned channels over large areas has been elusive. Here, we developed a new approach where the growth of cyclic peptide nanotubes can be directed in a structural framework set by the self-assembly of block copolymers. By conjugating polymers to cyclic peptides, the subunit of an organic nanotube can be selectively solubilized in one copolymer microdomain. The conjugated polymers also mediate the interactions between nanotube and local medium and guide the growth of nanotubes in a confined geometry. This led to subnanometer porous membranes containing high-density arrays of through channels. This new strategy takes full advantage of nanoscopic assembly of BCPs and the reversibility of organic nanotube growth and circumvents impediments associated with aligning and organizing high aspect ratio nano-objects normal to the surface. Furthermore, the hierarchical coassembly strategy described demonstrates the feasibility of synchronizing multiple self-assembly processes to achieve hierarchically structured soft materials with molecular level control.