I have never used Net::FTP::Recursive, but the documentation says:

This module's default behavior is such that the remote ftp server should understand the "dir" command and return UNIX-style directory listings. If you'd like to provide your own function for parsing the data retrieved from this command (in case the ftp server does not understand the "dir" command), all you need do is provide a function to one of the Recursive method calls. This function will take the output from the "dir" command (as a list of lines) and should return a list of Net::FTP::Recursive::File objects.

So, it seems to me that you could use ParseSub => \&foo and construct your foo such that it only returns directories in the list.