In this article an approach for assistance for soft tissue surgery through instrument navigation is presented. It can sufficiently be integrated into the clinical workflow. The presented methods are part of an assistance system for open liver surgery and supports surgeons during tumor resections or living donor liver transplantation. To combine preoperative CT data with intraoperative ultrasound images, the registration process is directly controlled by the surgeon through a 6D mouse (space ball). This simple yet effective approach overcomes existing limitations of automatic algorithms relying on stable image features within both ultrasound and CT images. As a first result, the described surgery assistance system was successfully applied in clinical routine.