This paper studied the post-processing process of the fused deposition modeling (FDM) process, one of the most widely used 3D printing technologies recently, in prototyping, which is a leading step in the development of various IoT products. The proposed post-treatment process is warm isostatic pressing (WIP), which can improve the mechanical properties and waterproof function of parts made by the FDM process. There are various process parameters in the WIP process, but in this study, the experiment was planned with the holding time of temperature and cooling ways as important variables. The specimens were manufactured in a direction that showed the most dramatic WIP effect, and in order to determine the effect of the WIP process, specimens without WIP treatment were manufactured and tested in the same manner. The experimental results confirmed that the WIP process improved mechanical properties and waterproofing effects. In addition, the temperature holding time did not affect the mechanical properties, and the mechanical change due to the difference in cooling method showed a 5% difference.