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3D skull is crucial in skull-based 3D facial reconstruction [1, 2, 3, 4, 5, 6, 7, 8]. In 3D reconstruction, especially in skull-based 3D facial reconstruction, features usually play an important role. Because, the accuracy in feature detection strongly affects the accuracy of the 3D final model. In this paper, we concentrate on accuracy of 3D reconstructed skull, one important part in skull-based 3D facial reconstruction. We discuss a cause of errors called shift errors when taking sequence of skull images. In addition, we analysis the effect of shift error in 3D reconstruction and propose solution to limit the effect.