3D printing, CAD/CAM-based processing approach, has been considered as an effective tool to satisfy the many requirements in the trends of manufacturing industry changing rapidly from mass production to mass customization. Fused deposition modeling (FDM), or material extrusion (ME) in ASTM terminology, has been one of the most commonly and widely used processes owing to its various advantages, such as low-cost material and hardware, simple processing mechanism, and wide material usage. Recently in the industry of 3D printing manufacturing fields, high-strength polymers with reliable performances have attracted much attention from the relevant researchers and engineers. In this presentation, we introduce the FDM-based 3D printing and the post-processing of polyetheretherketone (PEEK), which is one of the representative super engineering polymers. PEEK is the material as difficult to be processed as its high mechanical performance. We first developed custom-made 3D printing system, which was able to deal with the engineering plastic materials. Specifically, the 3D printer included several thermostatic control systems to modulate the environmental conditions of printing, such as the temperature of the surrounding air in the printing chamber. The use of temperature-controlled conditions in not only the nozzle but also in the chamber instead of room temperature was necessary in order to stably print the engineering polymers without defects or delamination in the final product. We studied the optimized parameters for the stable printing process, such as nozzle/chamber temperature, nozzle speed, printing tool-path, and extruding rate. With these process parameters, the maximum tensile strength of the resulting PEEK parts was achieved at approximately 80% of the bulk material property. In addition, we studied the effects of heat treatment on the mechanical property and crystallinity. The heat-based post-processing could improve the tensile strength up to 90% of the bulk material property, which was comparable to mechanical properties of bone. Based on the optimized conditions from process design to post-process, we tested the feasibility of manufacturing of orthopedic products and bone implants.