This paper concentrates on one probably most commercially significant AUV applications: Embedded Cable and Pipeline Tracking. A modular approach to this problem has been adopted as the AUTOTRACKER project. The research and development is partially funded by the European Union and companies within the offshore industry. The system is being demonstrated and evaluated on real offshore pipelines and cables using a commercial Survey-AUV. This paper describes AUTOTRACKER's modular, distributed software architecture. It then outlines the sensor and processing techniques used for real-time control of the AUV to perform tracking and obstacle avoidance. In addition, details of the system tests and practical trials used in the development process are outlined.