Hi,
In my experience, there's nothing wrong or difficult to work with only .stl files in FEFLOW. In fact, in my thesis I only used this kind of file.
Having said that, I suppose that you have a 'clean' non-manifold surface. Try to close it somehow, and assign region-markers to each enclosed zone. If you're using the tet-gen algorithm, it will generate different groups according to region-markers.