Systems and methods for conducting autonomous underwater inspections of subsea and other underwater structures using a 3D laser mounted on an underwater platform such as AUV, an ROV or a tripod. The systems and methods described herein can be used for scanning underwater structures to gain a better understanding of the underwater structures, such as for example, for the purpose of generating a 3D virtual model of the underwater structure. The 3D virtual model can be used for many purposes including, but not limited to, directing inspection, repair, and manipulation of the underwater structure, navigating around the underwater structure, and other purposes.