Over the past two decades, clear aligner therapy grew as an alternative to traditional brackets for orthodontic treatment. Recently, several orthodontic companies introduced their clear aligner brands, each with unique features such as material type and thickness, gingival trim design, specific auxiliary tools, and different strategies for guiding orthodontic movement. However, little is known about how these features impact their virtual treatment setup. This study aimed to compare the virtual treatment setups among five clear aligner companies to assess their differences. The initial records of 10 patients, including extra and intraoral photos and scans, were submitted to Invisalign®, ClearCorrect®, 3M™ Clarity™, Spark™, and Reveal® clear aligner systems. Each case prescription was standardized to ensure comparable treatment plans across the companies. The comparison focused on the number of aligners, number of attachments, amount of interproximal reduction per arch, planned extrusive or intrusive movement of maxillary central incisors, final canine and molar relationships, final intercanine and intermolar widths, and planned expansion or constriction of the intercanine and intermolar widths. Results indicated significant differences in the virtual treatment setups for the same patient among clear aligner companies in the number of aligners (p-value = 0.003), number of attachments (p-value < 0.001), and predicted final canine relationship (p-value = 0.013). However, no statistical differences were observed in the other variables evaluated. ClearCorrect® stands out by prescribing the fewest number of aligners and attachments, whereas 3M™ Clarity™ tends to prescribe the highest number of aligners and attachments. There is a notable deficiency across companies, particularly with ClearCorrect® and Spark™, in planning for a final bilateral canine Class I relationship. These findings suggest that the unique characteristics of each aligner company lead to distinct approaches in treating the same patient, highlighting both areas of discrepancy and consistency in the virtual treatment setups.