Three-dimensional (3D) in vitro models of cell culture aim to fill the gap between the standard 2D cell studies and the in vivo environment. Especially for neural tissue regeneration approaches where there is little regenerative capacity, such models must rely on scaffolds that mimic the extracellular matrix in providing support; allowing the natural flow of oxygen, nutrients, and growth factors; and possibly favoring neural cell regrowth. Their combined use with stem cells has many potentialities for tissue engineering applications. Here, we describe a new 3D model of stem cell culture, using a nanostructured biomaterial, made of self-assembling peptides, where adult neural stem cells are completely embedded. This new 3D cell culture system takes advantage of the nano- and microfiber assembling process of these biomaterials under physiological conditions. The assembled scaffold forms an intricate and biologically active matrix able to display specifically designed functional motifs such as RGD, BMHP1, and BMHP2. Such model has the potential to be tailored to develop ad hoc designed peptides for specific cell lines.