Assuming that you're using the Ethernet Shield (you didn't specify so I assume the standard device in this forum), you cannot implement IPv6 in software (library) because the Ethernet chip (WizNet5100) doesn't support IPv6. I'm not aware of an IPv6 implementation for the Arduino world. The easiest way is to use a Yun with a Linux system on the board that should support IPv6 (although I didn't check if it's activated).
PS: FTP over IPv6 sounds a bit like using a tank to transport a knight with a sword.