In complete denture fabrication, accurate preliminary impressions are crucial for obtaining an accurate final impression. However, it can be challenging in cases of atypical arch shapes. This case report compares diagnostic casts made with a stock tray and an intraoral scanner (IOS) in a patient with an atypical arch shape. A 58-year-old edentulous male patient with long, narrow, atypical arches was referred to the Oral and Maxillofacial Surgery department for complete denture fabrication. Compared to the diagnostic cast obtained using IOS with adequately captured anatomical parameters, the primary model obtained using a stock tray showed prominent overextended flanges on the labial and buccal sides of the maxillary arch and less prominent overextended flanges in the mandibular arch with pressure spots in the posterior palatal seal area. The custom tray fabricated from such a model required additional adjustment resulting in increased chair time during the final impression procedure.