Surgeons use different medical devices in the surgery, such as patient-specific anatomical models, cutting and positioning guides, or implants. These devices must be sterilized before being used in the operation room. There are many sterilization processes available, with autoclave, hydrogen peroxide, and ethylene oxide being the most common in hospital settings. Each method has both advantages and disadvantages in terms of mechanics, chemical interaction, and post-treatment accuracy. The aim of the present study is to evaluate the dimensional and mechanical effect of the most commonly used sterilization techniques available in clinical settings, i.e., Autoclave 121, Autoclave 134, and hydrogen peroxide (HPO), on 11 of the most used 3D-printed materials fabricated using additive manufacturing technologies. The results showed that the temperature (depending on the sterilization method) and the exposure time to that temperature influence not only the mechanical behavior but also the original dimensioning planned on the 3D model. Therefore, HPO is a better overall option for most of the materials evaluated. Finally, based on the results of the study, a recommendation guide on sterilization methods per material, technology, and clinical application is presented.