A method and system are described that can be used for scanning underwater structures. The method and system allow a user to gain a better understanding of an existing underwater structure. For example, the method and system allow for building a three dimensional model of an underwater structure. A sonar wave is directed toward an underwater structure, and a reflected sonar wave is received. Initial 3D data points are obtained from the reflected sonar wave, and are configured to provide a three-dimensional image of the underwater structure. A working alignment model of the underwater structure is generated by the initial data points. As new 3D sonar data is collected, the new 3D sonar data is aligned with and added to the alignment model.