Nano-precision machining using focused ion beam (FIB) is widely applied in many fields. So far, FIB-based nanofabrication for specific nanoscale applications has become an interesting topic to realize more diversities for nano-construction. Through FIB machining, we can easily achieve the required nano- and micro-scale patterning, device fabrication, and preparation of experimental samples. Nowadays, there is an increasing trend to learn from nature to design novel multi-functional materials and devices. Thus, more interestingly, another advantage of FIB is that it can be conveniently used to analyze the natural photonic structures, e.g., those in the butterfly which exhibits amazing optical phenomena due to sub-wavelength structural color. Accordingly, in the present study, structural analyses for butterfly wings were carried out using FIB. It is found that the photonic structures for the backside and frontside of the butterfly wing studied differ considerably. The difference accounts for the different colors on the dorsal and ventral sides of butterfly wings.