Not a user of CD3, but I know Gandwarf is and when he was trying to do this he could not do it within CD3 either, he ended up exporting the file to a JPG, then using Photoshop or GIMP to create the "elevated" look to achieve hills - I'm sure it could be just as easily done to create cliffs with waterfalls as well. I forget the name of the term, "bump map" maybe, create a copy of the map as a separate layer, done in grey scale then painting hills and valleys using the dodge and burn tool (white is high elevation and black is low elevation.)
I am sure that CD3 is not capable of doing that alone. You have to combine using multiple apps to achieve this.
Some one may be able to give you a more precise answer. I don't use GIMP or PS much beyond tweaking images, I use Xara Xtreme for all my mapping and can achieve what I need in there.
Final answer, you need to create the elevated illusion using an image editing program - you can't do this in CD3.
Hope that helps.
Edit: here is a link to Gandwarf's city maps, to see it done effectively to CD3 maps. http://www.cartographersguild.com/sh...warf+City+maps
Here is one tutorial on doing this in GIMP: