Copper-phthalocyanine (CuPc) thin films on MoS2 surfaces were investigated by noncontact atomic force microscopy (NC-AFM). Submolecular resolution was successfully obtained in both topographic and dissipation images of CuPc monolayers. For topographic contrasts, the influence of short-range chemical interactions is particularly considered while the dissipation contrasts are discussed in relation to the tip-induced molecular fluctuations. Molecularly-resolved NC-AFM image was also obtained on CuPc multilayer, which revealed the structural difference between the monolayer and multilayer surfaces. The energy dissipation measured on these surfaces showed distinctive difference reflecting the different structural stabilities in the films. Furthermore, local surface modification of CuPc monolayer was demonstrated by NC-AFM. This is a direct evidence for the existence of energy transfer from the vibrating cantilever to the molecules through dissipative tip–sample interactions.