References can be placed into Folders that you create and name. You can create folders on both the web and desktop versions of Mendeley.
On Mendeley web:
Under the My Library tab, click Create Folder. Name and save.
To place a reference into a folder, clico on the box next to the reference and then at the top of the column of references, click the drop down menu from Add select documents to... and choose appropriate folder.
On Mendeley desktop:
Under the menu bar, click the Folder icon containing the plus sign. Name and save.
To place the references into a folder just highlight and drag it to the appropriate folder.
In Mendeley desktop:
Select the folder which you'd like to search for duplicates
Go to Tools then Check for Duplicates
You will see a list of the duplicates, if any.
Select the document you want to see to verify whether to delete the duplicate.