Complex sentence: Since shape will differ between specimens, the observer has to manually go through and make sure the landmarks and semilandmarks are on the surface for each specimen and if not they must be moved to touch the surface, but this will still maintain the correct location.
Split into simpler sentences: Since shape will differ between specimens, the observer has to manually go through and make sure the landmarks and semilandmarks are on the surface for the rest of the specimens. If not they must be moved to touch the surface, but this process still maintains the correct location.