The birth deformity of ear, known as microtia, varies from a minimal deformed ear to the absence of auricular tissue or anotia. This malformation has been treated by reconstructing the external ear, mainly by autogenous rib cartilage in auricular repair. The fabrication of the ear framework is a prolonged reconstructive procedure and depends of the surgeon’s skill. In order to avoid these inconveniences and reduce surgery time, it was proposed in a previous work to use implants made with biocompatible materials. One of these is a scaffold made by fused deposition modeling using PLA based in the three-dimensional geometry of the ear cartilage. The aim of this work is to evaluate the feasibility of this scaffold to perform cell culture in a perfusion biorreactor by estimating the flow transport characteristics in porous media using a scaffold with the porous geometry of the human auricular cartilage for microtia. Flow and heat transfer through the scaffold were simulated by the lattice Boltzmann method, and permeability and shear stress distribution were obtained at different Reynolds numbers. The permeability values of the scaffold achieved are in the order of magnitude of scaffolds used for cell culture. Linear dependencies between maximum shear stress and Reynolds number, and between maximum shear stress and permeability were obtained. The values of shear stress achieved correspond to high percentage of cell viability. The scaffolds for microtia treatment with the proposed filling pattern select is appropriate for cell culture in a perfusion bioreactor with characteristics similar to those described herein.