Currently, well-known surgical procedures for bone defects are classified into four types: (1) autogenous bone graft transplantation, (2) allogeneic bone graft transplantation, (3) xenogeneic bone graft transplantation, and (4) artificial bone graft transplantation. However, they are often risky procedures and related to postoperative complications. As an alternative, tissue engineering to regenerate new bone often involves the use of mesenchymal stem cells (MSCs), derived from bone marrow, adipose tissues, and so on, which are cultured into three-dimensional (3D) scaffolds to regenerate bone tissue by osteoinductive signaling. In this manuscript, we provide an overview of recent treatment of bone defects and the studies on the creation of cell scaffolds for bone regeneration. Bone regeneration from bone marrow-derived mesenchymal stem cells using silica nonwoven fabric by the authors’ group were provided. Potential application and future direction of the present systems were also described.