Using bone scaffolds in regenerating damaged tissues is one of the common approaches in tissue regeneration and engineering. In recent years, three dimensional fabrication techniques have been extensively employed in fabrication of bone scaffolds. One of these methods is fused deposition modeling (FDM). However, one of the disadvantages of this techniques is the limited number of available materials. In this study, we have investigated the biocompatible materials suitable for development of bone scaffolds. Utilizing polymers such as poly lactic acid, poly caprolactone and thermoplastic poly urethane and mixing them at different ratios together with ceramic biomaterials such as nano-scale hydroxy aptite and diopside, we manufactured nano bio-composites which could be used in bone scaffold specimens. To increase the interaction between ceramic and polymeric phases, we used twin screw extruder. Then, this composite was used in fabricating a fiber with a suitable diameter to be used in fabrication of the bone scaffold utilizing the FDM technique. X-ray diffraction tests and dynamic light scattering were used to differentiate the ceramic material and to control the size of the components, respectively. The composites were further analyzed using differential scanning calorimetry. The mechanical properties of the composite were also studied using prototypes for tensile and compression tests of plastic materials. The experiments showed that the hydroxy aptite fabricated using Sol-Gel method resulted in a more homogenous structure. Also, the composite fabricated using equal amounts of PLA and TPU together with the ceramic phase of hydroxy aptite and a small amount of diopside can be an appropriate choice in fabrication of FDM filaments to be considered in bone scaffolds. Our study has shown that adding diopside to the composite containing PLA and PCL simultaneously can reduce the mechanical properties of the composite. Keywords Bone scaffold, Additive manufacturing, Fused deposition modeling, Poly lactic acid, Poly caprolactone, Hydroxy appatite