Purpose: This study was aimed to evaluate whether the size of the changed area included in the registration area affects the validity of superimposition in three-dimensional (3D) images. Materials and Methods: Ten mannequin heads which were sectioned to simulate maxillary and mandibular setback surgery were used. A total of 30 images, including 10 initial images, 10 images after moving both middle and lower faces, and 10 images after moving only lower face, were obtained. The 9 landmarks which consisted of the bilateral and midline landmarks of the upper, middle, and lower faces respectively were used. Each 3D image obtained after simulation was superimposed 3 times according to the different 3 registration areas. The one-way ANOVA and posthoc analysis were performed. Result: In the case of moving middle and lower faces, there was no significant difference in all markers when superimposition was performed based on no changed area and forehead area. However, in the case of superimposition by the whole face, all measurements showed a significant difference (P<0.05) except for Pn (P>0.05). In the case of moving only lower face, all measurements did not show a significant difference regardless of the registration area. Conclusion: The validity of 3D superimposition in 3D images could be affected by the size of changed areas included in the registration area. In the postoperative evaluation of mandibular surgery, the registration area does not affect the accuracy of the 3D superposition. However, after the maxilla-mandibular surgery, the registration area should be set except for the changed soft tissue.