So when you actually print it, the next layer is in the correct position for where the plastic ends up.
As people mentioned above, even though the plastic is extruded at the elevated position, gravity will pull it down to the surface of the raft. I know that's not a reasonable height to actually use.) I'm actually trying to use somewhere between. I'm including an example with a 1mm separation height (just for illustration purposes, so it's easier to see what's happening. The first layer after the raft prints at the right height, but the next layers print at a lower height, then move up from there. The Simplif圓D software doesn't seem to be handling the separation distance properly, though, for distances more than. I've tried replicating the MakerBot raft settings, since its rafts are fine. I've tried various raft separation distances with minimal success. I'm printing with PLA and find that I get much better adhesion with a raft, especially for very small parts.
I'm getting much more accurate parts with S3D, but much poorer removal of parts from the rafts. I got Simplif圓D because I needed better control over small part tolerances such as holes and parts that need to be assembled together after printing. I have a MakerBot Replicator 5 and have been using it with good success for several months.
