A vision guided intelligent system for automated crab meat picking operates in a fully automated or semi-automatic modes of operation using a crab meat picking routine based on (a) the CNN model localization of back-fin knuckles algorithm, and/or (b) the Deep Learning model which accurately locates not only knuckle positions, but also crab legs and crab cores, with a high pixel accuracy (up to 0.9843), and low computation time. The subject system uses a concept of analyzing crab morphologies obtained from digital crab images, and, using a Deep Learning architecture integrated in the system, segments crab images into five regions of interest in a single step with high accuracy and efficiency. The image segmentation results are used for generating crab cut lines in XYZ and angular directions, determining starting cutting points in Z plane, and guiding cutting tools and end effectors to automatically cut crabs and harvest crab meat.