The different between Remotely Operated Vehicle (ROV) and Autonomous Underwater Vehicle (AUV) is that ROV is connected with the main computer by the electronic cable, so the operator can control the vehicle depending on the environment showing on the monitor; However, AUV is dependent on the received data to autonomously respond the condition via controlling program. In our research, we wanted to use the General Purpose Controller, which had been developed in the previous experiment, in the mission-mode to construct our AUV system for remaining the original ROV controlling system and switching mode between AUV system and ROV system. The mission was divided into primary and secondary mission written by the txt file which is known as mission script, including execute time, target, and mission type etc. In addition, we used the Watch Dog Timer (WDT) in our AUV for the security procedure. When the mission is failed or over the setting time, the AUV will change to the security mode and go forward to the water surface. The other topic in this research wanted to use the Seafloor Laser Scanner (SLS), which was mounted on the AUV, to improve the scanning efficiency. However, when the scanner was working, the AUV had to maintain the stable altitude to the sea floor, so the accurately output power of thruster is needed to be considered and tested. In this part, we found out the properly controlling way in the small water tank first, and then checked the attitude and scanning system in the swimmer pool and towing tank in NCKU respectively, to prove the ability of SLS of AUV system.