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If the user has a lot of Saved Filters, they can use the "New Folder" option to organize them.
The user can find that option in the Available Trees Tools Menu by clicking on the plus sign 
and selecting New Folder when having the parent tree selected.
Once selected, the user will be prompted with the below popup to select a folder name.
Once created, the folder will appear under the parent Saved Filter tree, where the user can then select and drag and drop Saved Filters onto the folder to nest them in there.
If the user selects the Saved Filters first to be included in the same folder, then clicking to create a new folder, it will put them all in the same folder. The user won't have to drag and drop them in there.
The rest of the tool properties apply to the folder as well such as editing and deleting.