Hi Didier, FEFLOW maintains a minimum saturated thickness (0.01 meters?) in all elements because there is no such thing as a no-flow cell like in MODFLOW. The in/out flow on top is applied the top layer of the model no matter what mode is used. This can cause problems in the simulation if the layers vary in elevation much more than the observed water table. If you have to model such elevational changes, such as in a mountainous region, I recommend using 3D variably-saturated mode instead of phreatic. If you chose to use this mode, you will have to specify unsaturated properties that are compatible with your model setup.
Pete