HI,
There are very rare ways of doing it, better i would suggest you copy program which can copy a directory structure to FTP. Here is an example for this:
Referance:
http://splashtechie.blogspot.in
Apart from this solution the other option can be like, Parsing the directory and accordingly create folders at remote FTP server using your
java program and then copy the files to that folder created at FTP server. Even if it doesn't work last solution that i usually prefer is compress the folder with its content and send it to remote machine.