Popcorn maize (Zea mays everta) exhibits complex morphologies that challenge structural analysis. This study assessed the fidelity of the three-dimensional (3D) reconstruction and printing of four popcorn morphologies, unilateral, bilateral, multilateral, and mushroom, by integrating structured-light 3D scanning and (DIA), which can support the construction of food replicas. Morphometric parameters (projected area, perimeter, Feret diameter, circularity, and roundness) and fractal descriptors (fractal dimension, lacunarity, and entropy) were quantified as the relative ratios of printed/real parameters (P/R) to compare real flakes with their 3D-printed counterparts. Results revealed the lowest mean errors for Feret diameter (6%) and projected area (10%), while deviations in circularity and roundness were more pronounced in mushroom flakes. With respect to the actual mean values of the morphological parameters, real flakes showed slightly larger perimeter values (86 mm for real and 82 mm for printed objects) and a higher fractal dimension (1.36 for real and 1.33 for printed), indicating greater texture irregularity, whereas the projected area remained highly comparable (225 mm² in real/229 mm² in printed). These parameters reinforced that the overall morphological fidelity remained high (P/R = 0.9–1.0), despite localized deviations in circularity and fractal descriptors. Less complex morphologies (unilateral and bilateral) demonstrated higher structural fidelity (P/R = 0.95), whereas multilateral and mushroom types showed greater variability due to surface irregularity. Fractal dimension and lacunarity effectively described textural complexity, highlighting the role of flake geometry and moisture in determining expansion patterns and printing accuracy. Principal Component Analysis confirmed that circularity and fractal indicators are critical descriptors for distinguishing morphological fidelity. Overall, the findings demonstrated that 3D scanning and printing provided reliable physical replicas of irregular food structures as popcorn flakes supporting their application in food engineering.