We present a novel approach that achieves segmentation of subject body parts in 3D videos. 3D video consists in a freeviewpoint video of real-world subjects in motion immersed in a virtual world. Each 3D video frame is composed of one or several 3D models. A topology dictionary is used to cluster 3D video sequences with respect to the model topology and shape. The topology is characterized using Reeb graph-based descriptors and no prior explicit model on the subject shape is necessary to perform the clustering process. In this framework, the dictionary consists in a set of training input poses with a priori segmentation and labels. As a consequence, all identified frames of 3D video sequences can be automatically segmented. Finally, motion flows computed between consecutive frames are used to transfer segmented region labels to unidentified frames. Our method allows us to perform robust body part segmentation and tracking in 3D cinema sequences.