STL file exported and import to CFD model/ inlet create

Good morning everyone,

I have done the segmentation part of lower human airway. Now, I want to export it and then import to CFD model to simulate human airflow in the lower airway. However, when I export the model into stl file, and import it to spaceclaim for capping. The ansys spaceclaim cannot detect the whole on top of airway to cap. Has anyone done something like this before?
Please advice how you cap your model and setup inlet?

Thank you very much!