A system and method for determining intraoperative locations of a lesion in tissue from lesion locations determined in preoperative imaging includes determining three dimensional locations of surface features of the organ in the preoperative images. A preoperative surface map is extracted from stereo images annotated with surface features from preoperative images. An intraoperative surface map of the organ is extracted from stereo images, and surface features are identified in the stereo images corresponding to surface features annotated into the preoperative surface map. Three dimensional displacements of the surface features are determined and used to constrain a computer model of deformation of the organ. In embodiments, the model of deformation is adapted or constrained to model locations and dimensions of surgical cavities using an optical flow method and/or locations of surgical instruments in the organ. The model of deformation is used to determine intraoperative locations for the lesion.