In terahertz (THz) optical systems, polymer-based manufacturing processes are employed to ensure product quality and the material performance necessary for proper system maintenance. Therefore, the precise manufacturing of system components, such as optical elements, is crucial for the optimal functioning of the systems. In this study, the authors investigated the impact of various 3D printing parameters using fused deposition modeling (FDM) on the optical properties of manufactured structures within the THz radiation range. The measurements were conducted on 3D printed samples using highly transparent and biocompatible cyclic olefin copolymer (COC), which may find applications in THz passive optics for "in vivo" measurements. The results of this study indicate that certain printing parameters significantly affect the optical behavior of the fabricated structures. The improperly configured printing parameters result in the worsening of THz optical properties. This is proved through a significant change in the refractive index value and undesirable increase in the absorption coefficient value. Furthermore, such misconfigurations may lead to the occurrence of defects within the printed structures. Finally, the recommended printing parameters, which improve the optical performance of the manufactured structures are presented.