This in vitro study evaluated the impact of three inter-implant distances (7, 14, and 21 mm) on the trueness and surface distortion of models generated using intraoral scan bodies, as well as the misfit of milled structures assessed through scanning electron microscopy (SEM). Misfit at the multi-unit structure interface was also measured using digital radiography and SEM. Three typodont models with varying inter-implant distances were scanned (n = 10), and a reference scan was obtained using a desktop scanner. Trueness was evaluated through three-dimensional (3D) image comparisons. Five cobalt-chromium structures were milled for each group, and misfits at the mesial and distal faces of both implants were assessed using SEM and digital radiography. Statistical analysis was performed with α = 0.05. No significant differences were found in 3D trueness across the inter-implant distances (p = 0.373) or in mesial (p = 0.075) and distal (p = 0.720) misfit values of the most anterior implant. Similarly, no significant differences were found for mesial (p = 0.103) or distal (p = 0.426) misfit values of the most posterior implant. A strong correlation was identified between X-ray and SEM analyses of misfit (Pearson's r = 0.819, p = 0.045). Inter-implant distance did not significantly influence the trueness or fit of the milled structures. All milled structures adapted well to the implant abutments. The strong correlation between X-ray and SEM analyses suggests that digital radiography is a reliable tool for detecting misfit between milled structures and implants.