Orochimaru helped Madara get that face as well as develop the Rinnegan. This is partially why Madara activated the Rinnegan so late in his life; Orochimaru was the brain in the operation. As you can see, Orochimaru knew a lot of secrets, including Danzou's condition and Tobi's true identity.
There are small hints as the manga progresses all leading up to this point. Madara doesn't explicitly state it (in the below picture), but we know it is Orochimaru based on his research, Kishimoto's hints throughout the manga, and the fact Madara never met Kabuto before this war.
The underling is Obito and the acquaintance is Orochimaru (Ch. 657).
UPDATE: Here is the proof that Madara didn't know Kabuto. In the last 2 panels of the above pic, it is pretty much implied that Madara met a person (while he was alive) that showed him how to use his current technique. That person can only be Orochimaru.