Thrombosis is both attributed to biochemical agonists and mechanical stresses applied to platelets. Whilst the effect of biochemical agonists has been extensively studied, the mechanosensitive factors remain poorly defined. Stenotic microfluidic channels mimic the narrowing vessels, providing the real-time observation of platelets under disturbed flow. Though the experimental analysis of platelets in disturbed flow confirms the mechanosensitive behavior of platelets, it cannot explicate detailed thresholds for platelet activation. Computational Fluid Dynamics (CFD) could be utilized alongside experimental analysis to characterize thresholds for platelet behavior under imposed shear stress. CFD simulations, however, are prone to uncertainties and errors which should be minimized to obtain compelling results. Hereby, we have presented a CFD protocol for researchers in the field of microfluidic and hemodynamic studies.