That's an interesting idea, if you've made the negative print in two pieces, with alignment pins. Fill the mold, pop the halves apart and your head is in your hands!

Almost any 3D modeling program will allow boolean subtraction. Create the original model head, create a cube that represents the size of the negative mold, center or align as needed and subtract. Use a plane cut to split the negative mold into two pieces, keeping both (Meshmixer does this easily).

I would caution, though, that it will be substantially more difficult to remove the layer lines in a negative mold, even one printed in two pieces. You might get away with an epoxy wash/slosh to fill the lines, though.