This paper describes an adaptive extended Kalman filter (AEKF) approach for geo-referencing tasks for a multi-sensor system (MSS). The MSS is a sensor fusion of a phase-measuring terrestrial laser scanner (TLS) with navigation sensors such as Global Navigation Satellite System (GNSS) equipment and inclinometers. The position and orientation of the MSS are the main parameters which are constant on a station and will be derived by a Kalman filtering process. Hence, the orientation of a TLS/MSS can be done without any demand for other artificial targets in the scanning area. However, using inclinometer measurements the spatial rotation angles about the X- and Y-axis of the fixed MSS station can be estimated by the AEKF. This makes it possible to determine all six degrees of freedom of the transformation from a sensor-defined to a global coordinate system. The paper gives a detailed discussion of the strategy used for the direct geo-referencing. The AEKF for the transformation parameters estimation is presented with focus on the modelling of the MSS motion. The usefulness of the suggested approach will be demonstrated using practical investigations.