Fused deposition modeling (FDM), the most widely used additive manufacturing (AM) technology, is gaining considerable interest in the surgical sector for the production of single-use surgical devices that can be tailor-made according to specific requirements (e.g., type of patient surgery, specific shapes, etc.) due to its low cost, ease of access to materials (3D-printing filament), and the relatively low complexity. However, surgical 3D-printing parts should resist sterilization treatments without losing structural, mechanical, and dimensional accuracy. Thus, in this work, 3D-filaments based on poly(lactic acid) (PLA), poly(ethylene glycol-co-1,4-cyclohexanedimethanol terephthalate) (PETG), and a modified PETG material (CPE) were used to produce 3D-printed parts and further subjected to moist heat (MH) and dry heat (DH) sterilization processes as affordable and widely used sterilization processes in the medical field. The effect of MH and DH was evaluated by performing a complete mechanical, structural, thermal, and morphological characterization before and after both treatments. In general, the moist heat treatment produced a higher degradation of the polymeric matrix of PETG and CPE due to hydrolytic and thermal degradation, particularly affecting the tensile test and flexural properties. For instance, the linear coefficient of thermal expansion (LCTE) before glass transition temperature (Tg) increased 47% and 31% in PETG samples due to the MH and DH, respectively, while it increased 31% in CPE due to MH and was mainly maintained after the DH process. Nevertheless, in PLA, the MH produced an increase of 20% in LCTE value and the DH showed an increase of 33%. Dry heat treatment resulted in being more suitable for medical applications in which dimensional accuracy is not a key factor and there are no great mechanical demands (e.g., surgical guides).