You'll want to use Export and Import.
The Template Space is stored in the Repository as if it were a normal space i.e. in the Database and Content Store.
So, if you create a light template space with say 1 or 2 sub-folders, you can export that space to a .acp file. Export is available from 'More Actions' -> View Details -> Actions -> Export. Check "Include this Space". This creates a .acp file which itself can be saved to your local file system.
The .acp file is in fact in zip format, so if you unzip it, you'll see an .xml file. Inside the xml file, you'll see the definition of your template space. You can generate this xml for your 1000 folders and re-zip it. The resulting .acp file can then be imported in the templates folder.