We have known that Evernote can export and import notes with tags.
But .EnEx file has not tags tree structure information, so it will lose the tree structure when you import your .enex file.

Evernote Batch now provide new features to Export and Import tags with their tree structure.

Choose Evernote Tags with Their Tree Structure

In Evernote Batch:

1.     Click "Tag" tab -> "Structure" group -> "Export" command on Ribbon.
   
2.     Right click on Tag Tree, click "Check all" item.
   
3.     Click "Start" button to add checked tags into Export tree.