The benefit of autonomous vehicles in hydrography is largely based on the ability of these platforms to carry out survey campaigns in a fully autonomous manner. One solution is to have real-time processing onboard the survey vessel. To meet this real-time processing goal, deep learning based-models are favored. Although Artificial Intelligence (AI) is booming, the main studies have been devoted to optical images and more recently, to LIDAR point clouds. However, little attention has been paid to the underwater environment. In this paper, we present an investigation into the adaptation of deep neural network to multi-beam echo-sounder (MBES) point cloud in order to classify sea-bottom morphology. More precisely, the paper investigates whether fully convolutional network can be trained while using the native 3D structure of the point cloud. A preprocessing approach is provided in order to overcome the lack of adequate training data. The results reported from the test data sets show the level of complexity related to natural, underwater terrain features where a classification accuracy no better than 65% can be reached when 2 micro topographic classes are used. Point density and resolution have a strong impact on the seabed morphology thereby affecting the classification scheme.