Objectives. This study aimed to evaluate the effects of different cleaning regimes of acrylic-based removable orthodontic appliances on bacterial biofilm formation and whether the surface modification, i.e., polished acrylic fitting surface, reduces biofilm formation. Materials and Methods. This double-blind, parallel, randomized clinical trial involved thirty-nine orthodontic patients indicated for removable orthodontic appliances. The patients were allocated into three groups according to the cleaning method: brushing with a denture brush and chlorhexidine (CHX) toothpaste, Lacalut cleaning tablet, and a combination of both cleaning methods. Each patient wore an upper removable appliance containing eight wells fitted with eight detachable acrylic tiles (four polished and four unpolished) for seven days. Five types of oral microbiota were evaluated using selective growth media and biochemical tests. The biofilm cleaning efficacy was assessed using the colony-forming unit (CFU) and scanning electron microscopy (SEM). Statistical Analysis. Data from the CFU using different cleansing regimes were compared, following log transformation, using one-way analysis of variance (ANOVA). The polished and unpolished tiles were compared for biofilm formation on each cleansing method using an independent t-test. Results. There was no significant difference among the three cleaning methods on the polished or unpolished tiles. However, in polished tiles, streptococci were significantly reduced in all cleaning methods, whereas staphylococci and Staphylococcus aureus were markedly decreased in brushing and combination cleaning methods. However, the total number of anaerobic bacteria was significantly reduced in polished tiles using the combination method only. Conclusions. Polishing the fitting surface of an acrylic-based orthodontic appliance reduced the tested bacterial biofilm formation and may enhance cleaning efficiency. Brushing and combination methods showed superior cleaning effects compared to cleaning tablets. This trial is registered with NCT05707221.