We report on the design of practical surface enhanced Raman scattering (SERS) substrate based upon 3D alumina membranes with cylindrical nanopores chemically modified with polyelectrolyte coating and loaded with gold nanoparticle clusters. These substrates allow for a molecular-level, label-free detection of common plastic explosive materials (TNT, DNT) down to 5-10 zeptograms or 15-30 molecules and a common liquid explosive (HMTD) down to 1 picogram. Such a sensitive detection of organic molecules by utilizing efficient SERS substrates opens the path for affordable and label-free detection of trace amount of practically important chemical compounds.