Yes, press the download button to get a zip file out of the samples selected in the list, converted to the chosen export settings.
The contents of the zip will line up with the folder path above each sample name, so if you dropped folders in (nested folders are fine too), you’ll get folders out in the zip file.
You can also drop zip files or folders containing zip files and those will be processed too (there is a soft import limit of 750 files, which can be disabled in settings, but 750 is a good number to keep the ui responsive and the browser tab memory usage in check).