Processing of polymers plays an important role in application of polymers in biomedical engineering, for instance in manufacture of scaffolds for tissue engineering applications. Rapid prototyping technologies like fused deposition modeling (FDM) has been widely used in processing polymers for biomedical applications. The present work is focused on modeling of flow behavior in the extrusion liquefier in FDM. A finite element (FE) model of extrusion liquefier was constructed on ANSYS after verification of internal geometry using X-ray imaging. Polycaprolactone (PCL) is used as the base bio polymer for analysis. Experiments were carried out to characterize the physical properties like thermal conductivity, specific heat, viscosity and shear thinning property of PCL. These values were used for behavior modeling in the extrusion liquefier. The thermal and flow behavior in the extrusion liquefier is studied by varying input conditions and analyzing the velocity, pressure drop profiles at various zones of extrusion liquefier. Experimental values of parameters and the simulated flow model showed good correlation. The current model can be extended to predict the flow behavior of PCL/ Hydroxyapatite composites in a FDM head which in turn will reflect on the quality of scaffold constructed using the Biocomposite.