Regex for finding After Effects files in scene code format
root should be capitalized as it is a constant.
You can shorten the code by using sorted that returns a new list instead of working in place.
IGNORE in my opinion reduces readibility as it is less obvious than IGNORECASE.
Your regexes are pretty hard, I would extract them into constants and give them a name.
You make good use of list comprehensions, they shorten and simplify code, good job!
Performance may not be a primary concern here, but it is a good habit to use lazy generators: putting round parenthesis instead of square brackets outside the match comprehension will not build the list, saving memory and time. The same goes for scene_floders.