Self-organized anodic porous alumina films with hexagonal pore lattice have attracted a considerable attention for biological arrays and confinement of various organic probes dyes in solutions. A molecular structure with axial symmetry in bis-heterocyclic indole chains and conjugate system, such as cyanine fluorophore Cy3 dye, was investigated here with respect to its fluorescence when loaded in the anodic alumina pores.