The possibility of automatically classifying high frequency sub-bottom acoustic reflections collected from an Autonomous Underwater Robot is investigated in this paper. In field surveys of Cobalt-rich Manganese Crusts (Mn-crusts), existing methods relies on visual confirmation of seafloor from images and thickness measurements using the sub-bottom probe. Using these visual classification results as ground truth, an autoencoder is trained to extract latent features from bundled acoustic reflections. A Support Vector Machine classifier is then trained to classify the latent space to idetify seafloor classes. Results from data collected from seafloor at 1500m deep regions of Mn-crust showed an accuracy of about 70%.