This is fairly easy to do with OpenSCAD, but the STL you start with has to be watertight first, so make sure you run it through (for example) NetFabb's repair first. Here's sample code that imports an STL and slices off first a cube (to slice off the back of the head) then a sphere (to create a hollow). You'll need to play with the coordinates and sizes to make sure it does what you need to with your starting STL, and make sure you save the SCAD file to the same directory as the STL so OpenSCAD knows where to import from.

difference() {
import("HumanHead.stl");
translate(v=[-10,0,0])
cube(20,20,20);
translate(v=[-10,-10,0])
sphere(r=20);
}