The aim of this work is to evaluate computational models generated from multiple μCT scans with different parameters, to identify the most feasible scan combination for practical (minimized scan time) yet accurate (relative to highest resolution) biomechanical simulations. We segmented Weberian ossicle chains of Zebrafish and created 3D models from CT scan image stacks at 4.64 μm, 5.05 μm, 9.30 μm and 13.08 μm voxel resolutions. We used geometric morphometrics analysis to quantify inter-model shape differences and finite element modal and harmonic analyses to simulate auditory signal vibrations. Relative to the highest resolution and most accurate model, the Model 9.30 is closest in overall geometry and biomechanical behavior of all lower resolution models. We note that the differences in resolution (model 13.08) and quality (model 5.05) of the CT substantially affected the segmentation, reconstruction process and results of the 3D model of the ossicles. Therefore, we conclude that scan voxel resolution and contrast variations in CT images are a key factor influencing the results obtained in biomechanical simulations of delicate and minute structures.