To connect to an FTP server over ipv6, here is an example:
$ ftp fe80::a00:27ff:fe60:5885%eth0 2121
Connected to fe80::a00:27ff:fe60:5885%eth0
ftp is the protocol.
fe80::a00:27ff:fe60:5885 is the ipv6 address.
eth0 after % is the interface. This is because link-local addresses in many operating systems require the interface to be explicitly specified.
2121 is the port.