To sort references into folders with specific topics, select New Collection on the left toolbar and type in either the topic or project you would like the folder to be titled as.
You can also add sub-folders by creating new collections, then dragging and dropping them onto the name of the collection you would like the sub-folder to be under.
After a new collection is created, you can either drag or directly upload references into the folder through Mendeley Reference Manager or through Mendeley Web Importer. References can also be sorted in this manner for specific groups.