Several photogrammetric and geographic information system applications such as surface matching, object recognition, city modeling, environmental monitoring, and change detection deal with multiple versions of the same surface that have been derived from different sources and/or at different times. Surface registration is a necessary procedure prior to the manipulation of these 3D datasets. This need is also applicable in the field of medical imaging, where imaging modalities such as magnetic resonance imaging (MRI) can provide temporal 3D imagery for monitoring disease progression. This paper will present a general automated surface registration procedure that can establish correspondences between conjugate surface elements. Experimental results using light detection and ranging (LIDAR) and MRI data will verify the feasibility, robustness, and accuracy of this approach.