In the Zotfile preferences, if you choose "Custom Location" and leave it blank, it will rename PDFs in place, so you could attach PDFs as links to Zotero items regularly and then just use Zotfile to rename.

Alternatively, you could let Zotfile handle the sub folders. For that, choose the Custom Location and then specify how sub folders should be made (e.g., %A is for the first letter of the author; see full details at Zotfile.com).

I think I'm having similar problems as @andrewgangan: I have Zotfile set up to rename PDFs linked in Zotero to a Custom Location on my computer, but every time Zotfile "renames" the file, it actually just creates a duplicate file with the new name. How can I eliminate this duplication? @Joscha can you advise?

I'm having the same issue! Here is exactly what I did:

1. Using Chrome extension imported citation from Google Scholar into Zotero , but the fulltext pdf couldn't download without credentials, so...
2. Logged in through my university and downloaded pdf.
3. Dragged it into Zotero to link to citation.
4. Zotfile said to "click here" if I wanted to rename and move it to the Custom Location I've selected, so I clicked.
5. Zotfile indeed created a renamed file in my Custom Location, but the original pdf remained in the original folder I downloaded it to, so now it appears I have two copies of it, one nicely named and organized, and one with the original nonsensical file name.

What I am I doing wrong and/or misunderstanding about how this is supposed to work?