Find a perfectly flat piece of glass. Then using sandpaper (I started with 240, then used some 400 to smooth out any scratches) steadily rub the manifold across the surface until the dye/marker is gone (but don't go too nuts and take too much material off).

Even though these manifolds were new, I thought I'd check. Used manifolds subject to heat and overzealous manifold nut tightening would benefit greatly from this process.