Bones adjust their structure to withstand the mechanical demands they experience. It is suggested that flow-derived shear stress may be the most significant and primary mediator of mechanical stimulation. In this study, we designed and fabricated a fluid flow cell culture system that can load shear stress onto cells cultured on 3D scaffolds. We evaluated the effect of different culture techniques, namely, (1) continuous perfusion fluid flow, (2) intermittent perfusion fluid flow, and (3) static condition, on the proliferation of osteoblasts seeded on partially deproteinized bones. The flow rate was set at 1 ml/min for all the cells cultured using flow perfusion and the experiment was conducted for 12 days. Scanning electron microscopy analysis indicated an increase in cell proliferation for scaffolds subjected to fluid shear stress. In addition, the long axes of these cells lengthened along the flowing fluid direction. Continuous perfusion significantly enhanced cell proliferation compared to either intermittent perfusion or static condition. All the results demonstrated that fluid shear stress is able to enhance the proliferation of cells and change the form of cells.