We propose a fast shape decomposition method for granular microstructures using a 3-D approach based on medial axis. We define a two-step algorithm: the first step relies on a notion of digital flow to obtain a preliminary over-de- composition from medial balls. During a second step, we use geometric criteria to obtain a relevant and precise volumetric decomposition. We apply our al- gorithm to 3-D objects of materials and, more precisely, to microtomographic images of snow microstructures.