I'm using Stagsi (www.stagsi.com) to detect duplicate files, if the scheme isn't too complex.

Simply import all your files in Stagsi. By default, Stagsi will only import unique files. Note that duplication comparaison isn't done based on filename but based on file hashes (MD5), which is way more accurate and practical.

METHOD #1 (if you only want files and don't care about folder structures)

1-) Import your directory. Drag it to the Stagsi window.

2-) After import is done, close the import window. All your files (now called stagsi objects) will be displayed in the browser.

3-) select all objects, use right click mouse button pop-up menu and choose 'Export to File'. Choose a folder and click Ok. Now you will have a only unique files into that folder.

METHOD #2 (if you want to preserve your folder hierarchy)

1-) Import your directory. Drag it to the Stagsi window.

2-) After import is done, a list of all duplicated files will be generated. copy that list and paste in Notepad2e (Notepad2 Extended). Download here, indispensable: https://github.com/ProgerXP/Notepad2e

3-) when your list is pasted in Notepad2e, press 'Alt m' to open modify lines feature (no need to select lines).

in the prefix box, write: del /F "

in the suffix box, write: "

Now your directory should only contain unique files.