If the remote system is a UNIX based one, have the directories/files tar'd into a single file, then compress the file (gzip is good) for faster transmission.

If you do this, be sure and use binary mode for transmission.

Then, on the destination machine, you would need to uncompress and untar the file.

tar is a common way to put multiple files in multiple directories into a single file for transmission or distribution.

If both systems supported pkzip, that would do it also.

But ftp is a "File transmission protocol", and while it will handle wildcards, it will not cross directories.