Smart Fernandoes tend to mostly dive the enmy backline to distract and disrupt. When he dives th backline, this is your best opportunity to go for his backline and kill off his heavy damage dealers, especially while he regens with Last Stand.
Easy way to kill a fernando is to get behind the enemy and hit him from the back which will force him to turn around leaving him vulnerable to champions that were in front of him before,but you will have to be careful of his allies.