To create custom collections, click on the New collection box at the bottom of your list of collections, and give the collection a name. To create a hierarchical structure (collection and sub-collections), drag and drop the new collection to another collection, to sit within that collection.
You can drag and drop a reference from All References into a collection. The reference will also remain in All References.
Alternatively, you can select the reference (check the box to the left of it), and then in the Action panel at the bottom of the screen, click on Organize, then Add to Collection. You can specify multiple collections, to add a reference to.
If you remove a reference from a collection, the reference can still be found under All References.
To remove a reference from a collection, select it (click in the check box to the left of it), and then in the Action panel, select Organize, and then Remove from Collection.
Smart collections are automatically created by Mendeley, and cannot be renamed, repositioned or deleted:
To delete a reference, right-click on the reference and select Delete Reference, or drag-and-drop the reference to the Trash folder, which is found at the bottom of the list of smart collections in the left-hand pane.
References will remain in Trash unless you delete them permanently, or choose to restore them to your library. Click on Trash, and then select reference(s), by clicking in the check-box to the left. From the actions panel at the bottom of the screen, select either Delete permanently or Restore.