Background <p>Alignment accuracy in digital impressions is critical for implant-supported prostheses. This in vitro study evaluated the effects of scan body modifications and alignment software on digital impression accuracy.</p> Materials and methods <p>A printed maxillary model with a unilateral distal edentulous area included analogs at positions No. 25 and No. 27. Three scan body groups were tested: unmodified (M0), additive (M+), and subtractive (M−). Each was scanned 10 times using an intraoral scanner. Alignment was performed in Exocad and Medit Link software. Experimental scans were compared with a reference model using the best-fit method. Linear and angular.</p> Results&#xa0; <p>Mean linear deviations ranged from 0.04–0.07 mm and angular deviations from 0.23°–0.63°. Medit Link produced significantly lower deviations than Exocad (p &lt; 0.001, p = 0.001). Unmodified scan bodies showed the highest accuracy, and implant position also influenced results (p &lt; 0.001).</p> Conclusions <p>Both scan body modifications and alignment software significantly&#xa0;affected matching accuracy. Appropriate software can reduce implant&#xa0;misfits and improve prosthetic outcomes. These preclinical findings&#xa0;highlight the potential of advanced algorithms-based alignment&#xa0;approaches to enhance reliability under challenging conditions.</p> Clinical trial number <p>Not applicable.</p>