Background: Non-surgical mini-implant assisted rapid palatal expansion, or midfacial skeletal expansion, is a paradigm-shifting concept that in recent years has expanded the envelope of orthopedic movement in the transverse direction for adult patients. Although adding mini-screws to a rapid palatal expander is not complicated, accurate and successful expansion strongly depends on the device’s position and its relation to the resisting structures of the maxillofacial complex. Case presentation: This article presents a digital workflow to locate the optimal position of the Midfacial Skeletal Expander (MSE) device in a CBCT-combined intraoral scan file and describes how to transfer the MSE position intra-orally with properly sized bands during the device fabrication. The complete digital workflow of MSE fabrication and its application for a Class III orthognathic surgical case is presented in detail. Conclusions: This report describes a completely digital process that can accurately position the MSE device according to the orientation and morphology of maxillary basal bone, which is crucial in adult cases demand maxillary expansion.