This study presents the application of a polymer behavior model that considers fluid mechanics and heat transfer effects in a deposition system. The analysis of the polymer fluid properties is very important in the fabrication of precise microstructures. This fluid behavior model involves the calculation of velocity distribution and mass flow rates that include the effect of heat loss in the needle. The effectiveness of the proposed method was demonstrated by comparing estimated mass fluid rates with experimental values. The mass fluid rates under various process conditions, such as pressure, temperature, and needle size, reflected the actual deposition state relatively well, and the assumption that molten polycaprolactone(PCL) is a non-Newtonian fluid was reasonable. The successful fabrication of three-dimensional microstructures demonstrated that the model is valid for predicting the polymer behavior characteristics in the microstructure fabrication process. The results of this study can be used to investigate the effect of various parameters on fabricated structures before turning to experimental approaches.