Create folders to organize PDF files on Kindle?

Yes you can organize your Kindle books with “Collections”, not creating folders for them.

In fact, you have several ways:

1. Press and hold on a book’s cover at the library page, then choose add to collection. If you don’t have any collection created yet, it will ask you to create a new collection at first.
2. If the PDF files are stored in your Kindle cloud library, you can manage the collections more easily with Amazon’s web page, details please check this page: http://amzn.to/2rF3s6l
3. If your Kindle is jailbroken, you can manage the collections from computer, you can search on google with the query “calibre plugin manage kindle collection”