(1) Background: Thermoplastic materials are not inert and subject to changes in the oral environment, which affect their surface quality. Color stability and topographic characteristics of clear thermoplastic appliances are critical considerations. The study aimed to evaluate the optical changes and surface topography of different thermoplastic materials related to staining beverages and cleaning agents. (2) Methods: Thermoplastic polyethylene terephthalate glycol (PET-G) material specimens were selected for the study: S (Duran, Scheu-Dental GmbH, Iserlohn, Germany), D (Biolon, Dreve Dentamid GmbH, Unna, Germany), and B (Crystal, Bio Art Dental Equipment, Sao Carlos, Brazil). Four different media were involved for immersion: coffee (C) and black tea (T) at 55 °C, Coca-Cola (K) at 5 °C, and distilled water (W) at 22 °C. As for cleaning, chemical options and mechanical brushing were selected (P-powder, T-tablets, and X-brushing). Color changes, and mean surface roughness were measured at 24 h, 48 h, and after 7 days. Statistical analysis was performed. After the testing period, atomic force microscopy (AFM) analyses and SEM images were registered in order to characterize the surface topography. (3) Results: Quantitative color change evaluations revealed a slight change in color after 24 h and an extremely marked change after 48 h, respective 7 days. Mean roughness values are kept below the clinically acceptable limit of 0.20 µm for all samples. Related to mean nanoroughness values Sa, and 3D evaluations of the surface quality, Biolon samples have demonstrated the most constant behavior, while Crystal samples are visibly influenced by water immersion. Related to the cleaning method, the topography of Duran samples was influenced by mechanical brushing. (4) Conclusions: Nanoscale investigations provided high accuracy and more realistic surface quality examinations of the examined samples compared to profilometry. Both SEM and AFM should be used for a more detailed description of the surface topography.