Three-dimensional microanalysis of the microstructure of organic materials is important in the development and progress of novel materials on the micro-to-nanometer scales. We have developed the three-dimensional microanalysis method using focused ion beams (FIBs) for section processing (shave-off scanning) and mapping for time-of-flight secondary ion mass spectrometry (ToF-SIMS). Shave-off scanning can effectively create an arbitrary section on a sample set against composite materials with a wide variety of shapes; three-dimensional sample images are then obtained by alternately operating two FIBs. From the simulation results, we could set the optimum condition of beam irradiation. In this study, we confirmed the enhancement of secondary ion intensity by Au deposition under ToF-SIMS mapping with the optimized condition, and examine the usefulness of the simulation. The enhanced maps of characteristic polystyrene (PS) fragment ions were obtained. In addition, we observed the distribution of Au deposition by mapping results. These maps showed same tendency. The intensity of PS fragment ions was enhanced according to existence of deposited Au particles. These results indicated that a precise analysis of 3D MetA-SIMS can be realized.