Copper phthalocyanine (CuPc) thin films deposited on Au (111) surfaces were investigated by noncontact atomic force microscopy (NC-AFM). Structures with a periodic modulation of the spacing between the molecular rows of CuPc multilayer films were found. Submolecular features of each individual molecule on a film were successfully imaged. The obtained contrast was interpreted by the chemical interactions between a tip and the spatial electron density distribution of chemically active molecular orbitals such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). In addition, the energy dissipation in the NC-AFM imaging of monolayer films was studied on a molecular scale. The obtained high-resolution contrast in the dissipation images was discussed in connection with the random fluctuation of molecules.