The guy forgot to try to log into the ftp server itself to delete the files. After all, if the ftpd program used the correct APIs to create the directories and files, it would probably also use the right ones to delete them.
Judging by how the article was written, that probably wouldn't have helped him. You couldn't delete these directories directly, but rather had to delete the nested "unnamed" directory: “/path/to/COM1/ /“, which is also how you would create the directories in the first place. Usually, the tag-directory would also go along with a list of directories explaining that you should not create "undeletable" directories on NT-based servers, as that would annoy the admin and might cause them to remove anonymous access. You were only supposed to create large mazes of directories to prevent other random anonymous users from finding and deleting your files.