Whose eyes did Uchiha Madara use during the ninja war? I knew that Madara possesses the eyes of his brother to obtain Eternal Mangekyō Sharingan but is he still using those eyes during the Fourth Ninja World War? Or has he implanted different eyes?
Yes, he is still using Izuna's eyes. 

Those are the eyes with which he invoked the Eternal Mangekyo Sharingan and the Rinnegan.