Groundwater model as a tool is being used for various engineering applications. However, it is difficult to develop a groundwater model to truly represent a site condition with complex hydrogeological/geological conditions. A few aspects are addressed in this study: 1) multiple model layers should be used for a single hydrogeological unit in order to obtain more accurate solution to a groundwater flow system under certain conditions such as vertical hydraulic gradient are obvious and significant aquitards are present; 2) when the topographic surfaces changes sharply across the model domain, very fine and multiple layers can be used with flat model layer elevations that do not follows the natural unit surfaces as long as the hydraulic properties of various formation can be properly implemented in the model in the 3D domain. This approach proved to be numerically stable and more efficient using MODFLOW; and 3) multiple lines of evidences for model calibrations should be investigated when modeling groundwater flow systems with complex conditions to ensure the accuracy and representation of the model.