Recognizing material categories is one of the core challenges in robotic nuclear waste decommissioning. All nuclear waste should be sorted and segregated according to its materials, and then different disposal post-process can be applied. In this paper, we propose a novel transfer learning approach to learn boundary-aware material segmentation from a meta-dataset and weakly annotated data. The proposed method is data-efficient, leveraging a publically available dataset for general computer vision tasks and coarsely labeled material recognition data, with only a limited number of fine pixel-wise annotations required. Importantly, our approach is integrated with a Simultaneous Localization and Mapping (SLAM) system to fuse the per-frame understanding delicately into a 3D global semantic map to facilitate robot manipulation in self-occluded object heaps or robot navigation in disaster zones. We evaluate the proposed method on the Materials in Context dataset over 23 categories and that our integrated system delivers quasi-real-time 3D semantic mapping with high-resolution images. The trained model is also verified in an industrial environment as part of the EU RoMaNs project, and promising qualitative results are presented. A video demo and the newly generated data can be found at the project website1 (Supplementary Material).