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The shapes and morphology of the organs and tissues are important prior knowledge in medical imaging recognition and segmentation. The morphological operation is a well-known method for morphological feature extraction. As the morphological operation is performed well in hand-crafted image segmentation techniques, it is also promising to design an approach to approximate morphological operation in the convolutional networks. However, using the traditional convolutional neural network as a black-box is usually hard to specify the morphological operation action. Here, we introduced a 3D morphological operation residual block to extract morphological features in end-to-end deep learning models for semantic segmentation. This study proposed a novel network block architecture that embedded the morphological operation as an infinitely strong prior in the convolutional neural network. Several 3D deep learning models with the proposed morphological operation block were built and compared in different medical imaging segmentation tasks. Experimental results showed the proposed network achieved a relatively higher performance in the segmentation tasks comparing with the conventional approach. In conclusion, the novel network block could be easily embedded in traditional networks and efficiently reinforce the deep learning models for medical imaging segmentation.