An important challenge in the biomaterials field is to mimic the structure of functional tissues via cell and extracellular matrix (ECM) alignment and anisotropy. Toward this goal, silk-based scaffolds resembling bone lamellar structure were developed using a freeze-drying technique. The structure could be controlled directly by solute concentration and freezing parameters, resulting in lamellar scaffolds with regular morphology. Different post-treatments, such as methanol, water annealing and steam sterilization, were investigated to induce water stability. The resulting structures exhibited significant differences in terms of morphological integrity, structure and mechanical properties. The lamellar thicknesses were ∼2.6 μm for the methanol-treated scaffolds and ∼5.8 μm for water-annealed. These values are in the range of those reported for human lamellar bone. Human bone marrow-derived mesenchymal stem cells (hMSC) were seeded on these silk fibroin lamellar scaffolds and grown under osteogenic conditions to assess the effect of the microstructure on cell behavior. Collagen in the newly deposited ECM was found aligned along the lamellar architectures. In the case of methanol-treated lamellar structures, the hMSC were able to migrate into the interior of the scaffolds, producing a multilamellar hybrid construct. The present morphology constitutes a useful pattern onto which hMSC cells attach and proliferate for guided formation of a highly oriented extracellular matrix.