This paper gives an overview of our recent work on freely suspended layer-by-layer nanomembranes containing organized arrays of nanostructures such as carbon nanotubes or gold nanoparticles. These unique organized arrays toughen the membrane and add interesting optical properties which are useful in sensor applications. Gold nanoparticle encapsulated nanomembranes were characterized by surface enhanced Raman scattering, while those filled with carbon nanotubes were examined by resonance Raman scattering. Issues that are important to the fabrication, characterization, and applications of freely suspended polymer nanomembranes containing functional nanostructure arrays are discussed.