There are many possible solutions. None is perfect, but many of them work.
The one I still favour is the TreeCopyPlus plugin. Download and install the plugin as described in the readme. Create a custom column "dir" that shows the whole directory, then sort by that column. Now you got a list with all files, sorted by the folders they are in. Mark the files you want (no, you can't mark whole folders with one click with this solution) and then use TreeCopyPlus as packer.