1. A method for collecting and processing physical space data for use while performing an image-guided surgical (IGS) procedure, the method comprising: performing a rigid alignment of a computer model of a non-rigid structure of interest in a patient and surface data in a patient space associated with at least a portion of said non-rigid structure; and computing a deformation of the computer model that provides a non-rigid alignment of said computer model and surface data, said deformation computed using a set of boundary conditions defined for each node of said computer model based on said rigid alignment and a kernel function.