A system and method for registering a sequence of inter-operative two dimensional (2D) medical images of a target feature with pre-operative three dimensional (3D) medical images of the target feature is disclosed. The 3D image of the target feature is converted to a first skeletal graph. The 2D image of the target feature is converted to a second skeletal graph. Graph matching of the first and second skeletal graphs is performed to obtain a rough alignment of the graphs, and the first and second skeletal graph registered.