The main operation allows you to delete unused files and empty folder, it is possible to configure the main operation when launching it.
To know the unused files you have to add the assets you want to use in the "Assets Keep" list, then the program will search all the dependencies used by the assets you added, then it will search all the assets of the project to know the files to delete.
WARNING, this is how you use your reference system in your code, it is possible that some assets may not be found in dependencies, it is advisable to manually add the free reference like for example a class targeting.
Once you have made your list, the main process with all the options enabled in 'Delete Assets' works as follows:
Hard remove Assets : delete directly the files and in case of error delete the assets by "assets registry".
Get no assets File : finds the files that are not recognized as assets by your project, then offers to filter the files you want to delete.
Get empty Directory : finds all folders in the project that are empty, then in several passes it deletes the empty folders.
Assets checkout : optional that allows you to do a checkout on each remaining asset.
End info : displays the end of operation report.
Once the operation is finished it is possible that in the content browser you still see folders and assets that you wanted to delete, it is advisable to restart your project so that the editor reloads correctly the assets really present in the content folder.