“We had Peter in for a lifecast for episodes three and four [Under the Lake and Before the Flood] as we’d made prosthetics for the Ghost Doctor,” Kate Walshe, SFX producer at Millennium FX, told RadioTimes.com. “As we already had his lifecast, [producer] Pete Bennett and I discussed the possibility of making a skull based on Peter’s own face.
“We cast a version of Peter’s face out in clay and, following the contours of his distinctive bone structure, pared the form back to reveal what we imagine may be Peter’s own skull.”
It was his actual skull. (ish)