Dear Katy,
FaceGen matches photos by "fitting" our statistical model of shape and color, along with lighting and camera models, to make the best possible match to the photograph.
So no, we are not using a single template shape during this process but in fact a statistical model of shape variation encompassing many shape parameters.
Although this process is slower than other methods, it yields better results. Further, it allows for cool post-editing; for example of age, race and gender.
Best wishes,