The present study aimed to compare the thickness, gap width, and translucency of 3D-printed and thermoformed clear aligners using micro-computed tomography (micro-CT). Four groups of clear aligners were tested: thermoformed with single-layer material (TS, polyethylene terephthalate glycol) or a multi-layer material (TM, copolyester-elastomer combination), and 3D-printed TC-85 cleaned with alcohol (PA) or with centrifuge (PC). Aligners (n=10) were fitted onto respective models and micro-CT was performed. Thickness and gap width were measured for different tooth type in sagittal sections on all sides. CIELab coordinates were measured (n=5) to compare the translucency. Depending on tooth type and location, thermoformed and 3D-printed clear aligners have significantly varied thicknesses and showed a clinically acceptable range of fit with differences in regions of best fit. Centrifugation in post-processing significantly improved the translucency of 3D-printed aligners.