Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.