Polycaprolactone (PCL) is widely employed in biomedical applications. In this paper, the main goal is to propose new composites for fused deposition modeling (FDM) filaments to improve the properties of the current state of the art. Chitin-Nano-Whisker (CNW) and Nano-Hydroxyapatite (nHA) are employed as nanofillers in a PCL matrix to enhance the mechanical and biological properties of the scaffolds. FDM is an emerging production system in the manufacturing of bone tissue scaffolds. By proposing and characterizing the novel PCL/Nano-Hydroxyapatite/Chitin-Nano-Whisker composites, this paper attempts to improve the FDM products' capabilities to address the essential needs in the field. Mechanical analyses are performed based on ASTM standards, and the biological properties of the composites are assessed by employing MTT-assay on the composites using a bone cell line.