Each movie must be in a separate folder, so it sounds like you have the folder structure correct, but you must make sure the folder names are set up so the scraper can find the movies online. You should have it set up similar to this:
...\\Movies\\Back to the Future Trilogy\\Back to the Future (1985)\\Back to the Future (1985).mkv
...\\Movies\\Back to the Future Trilogy\\Back to the Future II (1989)\\Back to the Future II (1989).mkv
...\\Movies\\Back to the Future Trilogy\\Back to the Future III (1990)\\Back to the Future III (1990).mkv
The MB meta data scaper will get meta data for the movies, but not for the trilogy folder. You will have to download a folder and/or backdrop and place them in the "Back to the Future Trilogy" folder as folder.jpg and backdrop.jpg.
Maybe find one here.
If you are still having trouble, get your meta data with something like Media Center Master which will put the meta data and pictures in your movie folders, and rename the folders if it needs to.