You'll need povray installed as it is used to render the scene files produced. There is also a pov header file "header.pov" that defines the camera viewpoint. This should be written by the main program if it does not exist already.
When you run the threeD program you'll be presented with
a screen that will look something like this (cropped image
links to larger uncropped image).
This shows the images being generated. At the bottom of each image is a set of boxes and a number. The number indicates the current score. Use the "+" and "-" boxes to raise or lower the score. "G" saves the current gene and pov file generated to a subdirectory named "save-plants" and the leftmost box indicates either "R" for replace this, or "K" for keep it. The best strategy to evolve things usually involves scoring them well and marking them "K" to keep them (and their scores) around for a while.
Once you've scored as few or as many as you'd like, hit "regenerate" to go to the next "generation" and evolve a new set.
"Genepool" saves the whole current generation to a "genepool" which can be read in again for another run.
Two more images of the same run may be found here and here .