The ability to manipulate and direct neuronal growth has great importance in the field of tissue engineering, both for neuronal repair and potential medical devices. Imitating the 3D environment within a natural material is most important to simulate in-vivo conditions. Previously we have demonstrated that neurons grown on 2D patterned nano-topographic cues develop neurites aligned with the cues. We have also shown neurite growth is dependent on the material of substrate. Here we developed a method to grow neurons in a directed 3D environment. A collagen hydrogel system was chosen as a 3D ECM analog to best mimic the natural environment of cells. We compared the neuronal growth in 3D to a 2D model and showed that neurons in 3D collagen gels developed significantly longer dendritic trees and neurites. To align the collagen matrix, first, we induced controlled strain on the collagen gels. We were able to direct neuronal growth coinciding with collagen matrix orientation. Second, we embedded nanoparticles within the collagen gels and remotely controlled their orientation. The particles within the gel operated as mediators affecting collagen fiber orientation and also served as topographic cues to guide and modify neuronal growth. We showed a clear effect of the particle-based scaffold on the neuronal growth pattern. Both methods present a promising neuronal repair system in a realistic environment. Current efforts to implant these modified gels in injured neuronal models and to analyze neuronal recovery, at the single cell level, will be discussed.