The widespread use of three-dimensional (3D) printing technologies in medicine has contributed to the increased demand for 3D printing materials. In addition, new printing materials that are appearing in the industry do not provide a detailed material characterization. In this paper, we present the synthesis and characterization of polycaprolactone (PCL) based medical-grade thermoplastic polyurethanes, which are suitable for forming in a filament that is dedicated to Fused Deposition Modeling 3D (FDM 3D)printers. For this purpose, we synthesized polyurethane that is based on PCL and 1,6-hexamethylene diisocyanate (HDI) with a different isocyanate index NCO:OH (0.9:1, 1.1:1). Particular characteristics of synthesized materials included, structural properties (FTIR, Raman), thermal (differential scanning calorimetry (DSC), thermogravimetric analysis (TGA)), mechanical and surfaces (contact angle) properties. Moreover, pre-biological tests in vitro and degradation studies were also performed. On the basis of the conducted tests, a material with more desirable properties S-TPU(PCL)0.9 was selected and the optimization of filament forming via melt-extrusion process was described. The initial biological test showed the biocompatibility of synthesized S-TPU(PCL)0.9 with respect to C2C12 cells. It was noticed that the process of thermoplastic polyurethanes (TPU) filaments forming by extrusion was significantly influenced by the appropriate ratio between the temperature profile, rotation speed, and dosage ratio.