Separate Scenes into Books
This step is only necessary if the story is part of a series. If it's a standalone novel or novella, I skip this step.
That being said, this is where it gets tricky for me. I have to estimate how many books I'm going to have in the series. The problem is, there are still more scenes that will be added later on. Since I write fantasy, I want to keep each book at about 100,000 words. So I've worked out a formula that (mostly) works.
I estimate that each scene will contain about 1250 words. So each book would contain about 80 scenes. Since there are going to be more scenes added later, I figure about 40 scenes per book for the main storyline. So in the manuscript, I create a folder for each book: Book 1, Book 2, etc., and I put 40 scenes in each. If there are some left over at the end, I just stick them all in the last book, or if there are fewer than 40 (like 20 or more), I just put them in their own book.
Like I said, this is just an estimation to get an idea of how many books it will take to tell the story.