The present study compared the thickness and gap width of thermoformed and 3D-printed clear aligners (CAs) using micro-computed tomography (micro-CT) and evaluated their translucency using spectrophotometer. Four groups of CAs were tested: thermoformed with polyethylene terephthalate glycol (TS) or copolyester-elastomer combination (TM), and 3D-printed TC-85 cleaned with alcohol (PA) or with centrifuge (PC). CIELab coordinates were measured (n = 10) to evaluate translucency. CAs (n = 10) were fitted onto respective models and micro-CT was performed to evaluate the thickness and gap width. Thickness and gap width were measured for different tooth type and location in sagittal sections on all sides. The PC group showed significantly higher translucency than the PA group, which was similar to the TS and TM groups (p< 0.01). After the manufacturing process, thickness reduction was observed in the thermoformed groups, whereas thickness increase was observed in the 3D printed-groups. The TM group showed the least gap width amongst the groups (p< 0.01). Thermoformed and 3D-printed CAs had significantly varied thicknesses and regions of best fit depending on the tooth type and location. Differences in the translucency and thickness of the 3D-printed CAs were observed depending on the cleaning methods.