A system and method for registering 3D data sets is disclosed based on manual fiducial selection. The technique is useful in imaging obscured targets with 3-D imaging laser radars. For such an exemplary method, which defines a three-dimensional linear shift vector for each data voxel, four fiducials are required to completely define the mapping for a 3D space. An exemplary registration algorithm as disclosed provides an approach to automatically make fine adjustments to the 3D data registration. The tedious technique of shifting data sets relative to each other, in many degrees of freedom, is eliminated. Instead, a fine adjust is applied to the digital mapping function, through fiducial perturbation.