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Three-dimensionally-printed aortic templates are increasingly being used to aid in the modification of stent grafts in the treatment of urgent, complex aortic disorders, often of an emergency nature. The direct contact between the aortic template and the stent graft implies the necessity of complete sterility. Currently, the efficacy of sterilizing aortic templates and the effect of sterilization on the geometry of tubular aortic models are unknown. A complex case of aortic arch dissection was selected to prepare a 3D-printed aortic arch template, which was then manufactured in six popular printing materials: polylactic acid (PLA), nylon, polypropylene (PP), polyethylene terephthalate glycol (PETG), and a rigid and flexible photopolymer resin using fused deposition modeling (FDM) and stereolithography (SLA). The 3D models were contaminated with Geobacillus stearothermophilus broth and Bacillus atrophaeus. The sterilization was performed using three different methods: heat (105 °C and 121 °C), hydrogen peroxide plasma, and ethylene oxide gas. Before and after sterilization, the aortic templates were scanned using computed tomography to detect any changes in their morphology by comparing the dimensions. All sterilization methods were effective in the elimination of microorganisms. Steam sterilization in an autoclave at 121 °C caused significant deformation of the aortic templates made of PLA, PETG, and PP. The other materials had stable geometries, and changes during mesh comparisons were found to be submillimeter. Similarly, plasma, gas, and heat at 105 °C did not change the shapes of aortic templates observed macroscopically and using mesh analysis. All mean geometry differences were smaller than 0.5 mm. All sterilization protocols tested in our study were equally effective in destroying microorganisms; however, differences occurred in the ability to induce 3D object deformation. Sterilization at high temperatures deformed aortic templates composed of PLA, PETG, and PP. This method was suitable for nylon, flexible, and rigid resin-based models. Importantly, plasma and gas sterilization were appropriate for all tested printing materials, including PLA, PETG, PP, nylon, flexible and rigid resins. Moreover, sterilization of all the printed models using our novel protocol for steam autoclaving at 105 °C was also 100% effective, which could represent a significant advantage for health centers, which can therefore use one of the most popular and cheap methods of medical equipment disinfection for the sterilization of 3D models as well.