Numerous studies in tissue engineering and biomechanics use fluid flow stimulation, both unidirectional and oscillatory, to analyze the effects of shear stresses on cell behavior. However, it has typically been assumed that these shear stresses are uniform and that cell and substrate properties do not adversely affect these assumptions. With the increasing utilization of fluid flow in cell biology, it would be beneficial to determine the validity of various experimental protocols. Because it is difficult to determine the velocity profiles and shear stresses empirically, we used the finite element method (FEM). Using FEM, we determined the effects of cell confluence on fluid flow, the effects of cell height on the uniformity of shear stresses, apparent shear stresses exhibited by cells cultured on various substrates, and the effects of oscillatory fluid flow relative to the unidirectional flow. FEM analyses could successfully analyze flow patterns over cells for various cell confluence and shape and substrate characteristics. Our data suggest the benefits of the utilization of oscillatory fluid flow and the use of substrates that stimulate cell spreading in the distribution of more uniform shear stresses across the surface of cells. Also we demonstrated that the cells cultured on nanotopographies were exposed to greater apparent shear stresses than cells on flat controls when using the same fluid flow conditions. FEM thus provides an excellent tool for the development of experimental protocols and the design of bioreactor systems.