This work focuses on the creation of high resolution micro-bathymetric maps using a high frequency pencil beam sonar. These maps typically cover areas of 10's to 100's of square meters. Data is collected using a sonar mounted to an underwater vehicle that can be positioned at discrete locations on the sea floor or flown in a survey pattern above the bottom. Specifically, we are focused on improving the accuracy of these terrain maps by merging sonar pings taken from multiple vantage points over the same location. This requires the adaption of data registration techniques to handle errors related to the sonar sensor. The registration can also be modified to incorporate the navigation data available from an instrumented underwater vehicle. A two axis scanning sonar was used to gather data in the form of densely sampled range images. The data registration works on the 3D projection of these range images in a scan-matching manner. Through this process regions occluded in a single scan are filled with data available from other scans and individual pings which show a poor return are removed. Refined estimates of the scan vantage points are also generated during the registration. The initial estimates of these locations are provided by navigation data. The practical application of this work complements photographic mapping when visibility is limited. It also provides additional measurements which can be used to improve vehicle navigation.