The REPRAP tool chain uses a small collection of software to take a 3D model from a design to a physical object.
The 3D Printer microcontroller is loaded with a firmware that controls the machines behavior. This firmware must be setup manually with the correct thermistor, estep, and other printer specific settings.
We suggest Marlin (GitHub) Zip download
The firmware is edited with the Arduino IDE.
We provide a custom version for the MendelMax 2.0 at: http://www.makerstoolworks.com/support-and-docs/download-center/
Now onto printing a 3D Model.
First, you create your model and save it as an STL. You can use pretty much any 3D modeling software from SketchUp to SolidWorks.
Next, you will slice the model into a gcode file. This is basically the machine code directing the nozzle. We recommended Slic3r
Last, you need a way to send the gcode to the printer. For this a host controller software is used. Our favorite is Printrun, sometimes called Pronterface. http://reprap.org/wiki/Printrun
You can download a precompiled version here: http://koti.kapsi.fi/~kliment/printrun/
Another new host software is Repetier, it has a nice UI, however it is new and a few bugs do exist. Check it out at: http://www.repetier.com/
Here is a great overview of the path from an idea to an object:
Infographic Step by Step Guide for 3d Printing with a Reprap