Three-dimensional microanalysis of the microstructure of organic materials is important in the development and progress of analytical methods on the micro-to-nanometer scales. We have developed a novel three-dimensional microanalysis method using focused ion beams for section processing (shave-off scanning) and time-of-flight secondary ion mass spectrometry for mapping. Shave-off scanning can effectively create an arbitrary section on a sample set against composites materials with a wide variety of shapes; three-dimensional sample images are then obtained by alternately operating two focused ion beams. In this study, we adapted metal-assisted secondary ion mass spectrometry for three-dimensional microanalysis. We have devised a unique method whereby gold is deposited on a section to be analyzed after every shave-off sectioning by setting a gold plate at the back of the sample. Consequently, gold was observed to be deposited on the created cross-section concurrently with shave-off sectioning, resulting in a substantially enhanced secondary ion intensity. Copyright © 2014 John Wiley & Sons, Ltd.