You'll have to violate the iso9660 standards but it is necessary if you want to preserve your filesystem and filenames and shouldn't be an issue as long as you are using a modern OS like Linux.
genisoimage -o Backup-Myfiles.iso -r -J -joliet-long /some/path/
You will get errors like below (even enabling joliet-long didn't help)
genisoimage: Error: /some/filename.pdf have the same Joliet name
Joliet tree sort failed. The -joliet-lo........