Stable multilayer films have been fabricated on the basis of alternating layer-by-layer assembly of an azulene-based supra-amphiphile and a photoreactive polyanion. Moreover, one component of the supra-amphiphile, pyrene, can be removed from the multilayer films, generating functional surface-imprinted multilayer films. Uptake experiments show that the surface-imprinted films are capable of recognizing the hydrophobic template molecule in water. The reloading process increases with increasing of temperature. The loading capacity can be regulated by change of the layer pairs. In addition, the as-prepared multilayers are promising in purification of pyrene-polluted water.