The article describes some of the purpose behind NE-1: to build and test mechanical models of molecular machines.
Page 110 shows a design I hadn't seen before -- a combined pump and purification system for acetylene (inspired by the Drexler/Burch nanofactory video). This is very cool, and although it's an early proposal, it may begin to answer questions that have been raised about how to purify feedstock in nanofactories.
The article briefly describes several features of NE-1, including the ability to build certain molecules such as buckytubes by just entering a few parameters.
At the end, it also announces that a forthcoming version of NE-1 will output DNA sequences for Rothemund tiles. You will be able to design your tile in the program, then send the output file to a DNA-synthesis company, and get back DNA you can use to actually build the shape you just designed.
(I am on Nanorex's Science Advisory Board, and an alpha tester of NE-1, which I can confirm is a really fun and interesting program.)