Clear aligners are becoming a popular mode of treatment in orthodontics. Despite their increase in use and demand, there is a general lack of literature regarding the fundamental intrinsic mechanical properties of clear aligners. Therefore, it becomes difficult for patients and clinicians to compare the performances of different aligner products. Existing studies have investigated the biomechanical properties of raw plastic sheets used to make aligners, and sheets thermoformed over simple geometries (i.e. standard blocks). However, the results obtained from standard blocks have limited clinical significance. Instead, aligner samples with actual dental morphology need to be tested to yield clinically meaningful data. Therefore, the aim of this study is twofold. First, we set forth a standardized protocol to characterize significant properties of both raw thermoplastic sheets and fabricated aligners. Second, we evaluated the effects of processing and intraoral components on the aligner materials. These components include heat treatment during aligner manufacturing processes, water soaking, and pH alternations.To characterize the mechanical properties of the thermoplastic sheets and fabricated aligners, we first characterized the structural compositions of aligners by measuring the degree of crystallinity of each material. Second, we used TA Instruments� Dynamic Mechanical Analyzer (DMA) to quantify critical properties such as stress relaxation and creep of aligner samples with high accuracy and precision. Third, we compared strength and resistance from macroscopic and microscopic levels to analyze crack resistance and microhardness. We also measured Arrhenius activation energy and glass transition temperature to study physical phase transition and molecular interactions after thermomechanical changes. Moreover, we mapped out thickness distributions and quantified the light transmission of different aligner materials. Lastly, we examined the effects of heat treatment and water-polymer interactions on the aforementioned mechanical properties. Our findings suggest that thermoforming processes reduced aligner thickness and stiffness, increased hydrophilicity and water absorption, modified crack resistance, transparency, glass transitioning temperature, and microhardness in some materials. Water soaking resulted in reduced initial stress and Arrhenius energy, but increased stress relaxation and creep compliance compared to the unsoaked controls. Aligners with different chemical compositions exhibited distinct mechanical characteristics and responded differently to the changes in heat treatment and water soaking. In summary, we found that heat treatment and water immersion can lead to significant degradation of various important mechanical and thermal properties of aligners. Thus, the clinical performances of aligners may be affected by thermoprocessing and intraoral use. The long-term goal is to share our protocols with other independent institutions so that we can create collaborative monitoring and analysis of all aligner products in the market. The clinical impact is to improve patient care by allowing clinicians to make evidence-based decisions in material selection.