Folders allow you to organise your references into logical groups.

Folders may contain sub folders and can be added and deleted as required.

This 1 minute video will show you how to create folders.

References can be added to a folder by clicking and dragging them from another folder.

References in a folder can be removed by right clicking on the reference and selecting Remove from Folder.

Note!  The reference will still be in the All Documents folder.

You can remove a whole folder by right clicking on it and selecting Remove Folder.

Note!  The references will still be in the All Documents folder.

The following text is copied from Mendeley's Mendeley Reference Manager Help Guide

Custom Collections

Custom collections offer a way to quickly filter the view of your library.

Adding a reference to a collection in your Mendeley library does not relocate the reference, but instead acts as a label. This means that any reference added to a collection will still appear in ‘All References’. If you delete a collection the references inside will still be available in ‘All References’.

To create a new collection, select the ‘New Collection’ button in the left hand navigation panel.

To add a reference to a collection, drag and drop it onto a collection in the left hand navigation panel.

Note: Custom collections are essentially the same feature as 'Folders' in Mendeley Desktop. If upgrading from Mendeley Desktop to Mendeley Reference Manager, your 'Folders' will appear as 'Collections' in Mendeley Reference Manager

Mendeley Desktop has a feature to locate potential duplicate references in your Mendeley library, and merge them.
When adding references to your Mendeley library over time from multiple sources (OneSearch, Google Scholar, databases etc), it is possible to accidentally import the same reference more than once. It is important to remove these duplicate references regularly to avoid complicated issues in your Word documents.

When there are duplicate references in your Mendeley library, it is easy to accidentally insert both of the duplicates into a Word document. This results in the reference appearing twice in your reference list/bibliography, and can cause errors in your referencing. The referencing style will format the references as two separate documents, instead of repeat references to the same document (eg; Author, 2021a and Author, 2021b in APA style). The only way to resolve this is to manually search your Word document for all instances of the duplicate reference, remove them and replace them with the original copy of the reference. Multiply this issue by several duplicated references and it becomes very time-consuming to resolve! Removing duplicates in Mendeley regularly prior to inserting references in Word prevents this.

Mendeley Reference Manager (as of version 2.93)

Duplicated references are grouped into sets and can be found in 'Duplicates' on the left hand navigation panel. Any duplicated references can be deleted within the set. 

When new references are being imported and duplicated references detected, a prompt button appears, which when clicked, will direct you to the 'Duplicates' area. You would then be able to review and delete any duplicated references. 

Mendeley Desktop

In Mendeley Desktop, click the Tools menu, and select the option 'Check for Duplicates'.

Mendeley will display "sets" of documents which have potential duplicates. A "set" is any number of documents which have some identical information, such as identical titles and authors, and therefore may be duplicate references to the same document.

In the Details section on the right, Mendeley will indicate if the potential duplicates are completely identical, or if there are any 'conflicts' where copies have different information.

If the references are identical duplicates, click the Confirm Merge button. Mendeley will move to displaying the next set in the list.

In the above example, 'Author' is not ticked, indicating a conflict. When the set is expanded, we can see one copy of the reference has the author's initials as "S.J. J", while the other has just "S.J."

If there are conflicts, you will need to decide which copy has the correct information before merging.

The following guidance on how to manage duplicates with conflicts is copied from this article on Mendeley's support hub.

1. If any un-checked field looks incorrect, you can edit the field as you would normally, to input the correct data.
2. Alternatively, if you know that one of your duplicates had the correct metadata, but Mendeley has picked the wrong data for some reason, you can expand the set by double clicking (or clicking the expand arrow to the left), select the correct document, and tick the box next to the metadata you want to use. You can pick and choose data individually this way from any documents in the set, but be aware that when you check a box here, it will overwrite what was previously selected as the correct data for the merge.