In this paper we present (1) analysis of imaging sonar measurement for two-view relative pose estimation of an autonomous vehicle and (2) bundle adjustment and 3D reconstruction method using imaging sonar. Sonar has been a popular sensor for underwater application due to its robustness to water turbidity and visibility in water medium. While vision based motion estimation has been applied to many ground vehicles for motion estimation and 3D reconstruction, imaging sonar addresses challenges in relative sensor frame motion. We focus on the fact that the sonar measurement inherently poses ambiguity in its measurement. This paper illustrates the source of the ambiguity in sonar measurements and summarizes assumptions for sonar based robot navigation. For validation, we synthetically generated underwater seafloor with varying complexity to analyze the error in the motion estimation.