if your system uses full disk encryption (such as via LUKS) and you simply copy files off to an external or a secondary drive for a ‘backup’, no. the copy is not encrypted unless the destination has encryption set up on it, too.
the alternative would be using a backup program, instead of a simply file copy, that encrypts its backups.
easy to use gui backup utilities (like pika and déjà dup) can also encrypt its backups