Fluorescent and transparent polymer films with exquisite micro-structures are ideal candidates for anti-counterfeiting tags. However, it is still a great challenge to embed such properties in one breath figure array due to the restriction of the film-forming ability of polymers. In this work, we designed and synthesized fluorescent copolymers from styrene and 1-pyrenylmethyl methacrylate (PYMMA) and studied their self-assembly behaviors via the breath figure method. The significance of end groups and topologies have been investigated in detail. Novel hexagonal breath figure arrays with high transparency are formed at extremely low concentration (down to 0.06 mg/mL). The breath figure arrays display blue honeycomb pattern when irradiated by ultraviolet light. Breath figure arrays with such special optical properties demonstrated an ideal solution for anti-counterfeiting tags. Besides, this work demonstrates the significance of polymer architecture on the morphology of breath figure arrays and may enlighten the polymer design for a broad range of applications. • Fluorescent copolymers were designed and synthesized for self-assembly by the breath figure method. • A highly regular breath figure array can be formed at polymer concentration of as low as 0.06 mg/mL. • Transparent and fluorescent breath figure arrays are potential for anti-counterfeiting. • Effects of end groups and topologies of polymers on the morphology of breath figure arrays were studied.