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Craniofacial superimposition (CS) is a forensic process where photographs or video shots of a missing person are compared with the skull that is found. By projecting both photographs on top of each other (or, even better, matching a scanned 3-D skull model against the face photo/video shot), the forensic anthropologist can try to establish whether it is the same person. The whole process is influenced by inherent uncertainty, mainly because two objects of different nature (a skull and a face) are involved. In this paper, we extend our previous evolutionary-algorithm-based method to automatically superimpose the 3-D skull model and the 2-D face photo with the aim to overcome the limitations that are associated with the different sources of uncertainty, which are present in the problem. Two different approaches to handle the imprecision will be proposed: weighted and fuzzy-set-theory-based landmarks. The performance of the new proposal is analyzed, considering five skull-face overlay problem instances that correspond to three real-world cases solved by the Physical Anthropology Laboratory, University of Granada, Granada, Spain. The experimental study that is developed shows how the fuzzy-set-based approach clearly outperforms the previous crisp solution. Finally, the proposed method is validated by the comparison of its outcomes with respect to those manually achieved by the forensic experts in nine skull-face overlay problem instances.