The flow of complex fluids in confined geometries produces rich and new phenomena due to the interaction between the intrinsic length-scales of the fluid and the geometric length-scales of the device. In this talk, I will choose a wormlike micellar model system to illustrate the idea. I will focus on a micellar solution that yields a novel route to synthesizing bio-compatible nanoporous sol-gels. Through a combination of experiment and modeling, I will show how self-assembly, confinement, and flow can be utilized to control fluid microstructure and system phase transitions, and thus to enhance the controlled synthesis of bio-compatible new materials.