Polymethylmethacrylate (PMMA), Polycarbonate, (PC), and Polyetheretherketone (PEEK) are thermoplastic polymers with properties that have already been proved favorable for bio-medical applications. They have been applied in different medical fields such as maxillo-facial surgery, orthopedic surgery, intraocular surgery, and more, due to their mechanical properties, and osteoinductive and antimicrobial capabilities. As these polymers become important biomaterials for bone and cartilage replacement, the optimization of the manufacturing processes seems more relevant than ever. The adaptability of the 3D printing process allows for the manufacturing or building of the desired piece with the exact characteristics, shape and size for each individual, in a way that they may be built or modified very easily. The result is that biomedical application options are increased with the utilization of 3D printing techniques. In this work, we have studied the effect of heat treatment on the mechanical properties of 3D printed samples prepared with the three different polymers. By selecting the right printing temperature, as well as heat treatment process, the mechanical properties can be tailored specifically for different applications. It is critical to make comparisons between the mechanical properties of hard and soft tissues, and compare them to the ones of typical metallic, ceramic and polymeric biomaterials. Furthermore, by researching and optimizing the properties of 3D printed polymers, a comparison can be made with the implants commonly made using molding processes and consequently modulus of elasticity, hardness, and other properties can be optimized to make them suitable to be used as various biomedical devices.