Can't talk to the CM, but the Prolimatech Megahalems requires a bit of minor trimming on the case window fan in the Antec 1200. The CM one is slightly taller by 2.4 mm and is wider
CM - 120 x 128 x 161.1mm
MH - 130 x 74 x 158.7 mm (130 x 124 x 158.7 w/double fans)
So yes, I'd expect an issue unless you MoBo puts the chip significantly farther away than the Asus R2E.