Twin screw extrusion (TSE) is one of the commercially established processes for reinforcement of metallic/nonmetallic/ceramic fillers in polymer matrix for tailor-made applications. In this study, biocompatible feedstock filament has been prepared (in-house) for commercial fused deposition modeling (FDM) setup with biocompatible grade polymers, namely polyvinyl chloride and polypropylene which was reinforced with the hydroxyapatite particles. The process parameters (namely, material composition, rotational speed of TSE, die temperature of TSE, HAp particle grain size, and applied load on TSE) were optimized using Taguchi L18 orthogonal array. In this study, mechanical, thermal, and metallurgical properties have been established, and best-feedstock filament wire for development of partial/complete denture on the FDM with functionally graded surfaces properties has been recommended for future applications.