EmptyFolderDeleter.cs

using System.IO;
using UnityEditor;

public static class EmptyFolderDeleter
{
    [MenuItem( "Tools/Delete Empty Folder" )]
    private static void Delete()
    {
        DoDelete( "Assets" );

        AssetDatabase.Refresh();
    }

    private static void DoDelete( string path )
    {
        foreach ( var dir in Directory.GetDirectories( path ) )
        {
            DoDelete( dir );

            var files = Directory.GetFiles( dir );

            if ( files.Length != 0 ) continue;

            var dirs = Directory.GetDirectories( dir );

            if ( dirs.Length != 0 ) continue;

            AssetDatabase.DeleteAsset( dir );
        }
    }
}