3D porous Ti6Al4V scaffolds were directly fabricated by a rapid prototyping technology, 3D fiber deposition (3DF). In this study, scaffolds with different structures were fabricated by changing fiber spacing and fiber orientation. The influence of different architectures on mechanical properties and permeability of the scaffold were investigated. Mechanical analysis revealed that compressive strength and E-modulus increase with decreasing the porosity. Permeability measurements showed that not only the total porosity but also the porous structure can influence the permeability. 3DF was found to provide good control and reproducibility of the desired degree of porosity and the 3D structure. Results of this study demonstrate that the 3DF of Ti6Al4V give us flexibility and versatility to fabricate and improve scaffolds to better mimic the architecture and properties of natural bone and meet the requirements of bone graft substitutes and orthopedic and dental implants.