Submarine geotechnical exploration is a challenging task that is currently undergoing a paradigm change thanks to robotics and teleoperation. The MD500 Project is an underwater subsea geotechnical drilling and in situ testing device designed to sample and probe up to 150 m of soils of rock beneath the seabed in water depths of up to 500 m. The system has applications in several areas of marine activity, such as port infrastructure, nearshore and offshore renewable energy projects, oil & gas, submarine mining, etc. The machine consists of a group of devices operated remotely and that must synchronize with each other: drilling tower, stabilizing legs and three manipulators (two cartesian and one anthropomorphic). These manipulators can be operated manually or in a semi-automated (robot) mode. The automated routines aim to substitute the actions of the drilling crew when handling the tubes and rods in the harsh environment for which the machine is envisioned The paper presents an overview of the code and logic behind the tool manipulation and handling routines of the MD500, which are at the core of a