2. CAM for FDM

Q: How does a STL get turned into a file i can print
A: CAM - Makeware

The Replicator 2 requires the use of either Makerware or Replicator G to "Slice" [a type of CAM]  from an STL file to a Gcode file.

There are setting to control the material properties and aid building the "thing":
Quality: The finer the quality the smoother the surface, and finer the detail. 3X finer takes at least 3X longer to build and slice.
Raft - this is a big plate of loose material attached to the build plate that will support tall objects. 
Supports - Supports can be generated by the slicer or you can add them to your model where needed. Use Support anywhere "undercut" or "overhang" will not bridge to another supported point.
In fill - The interior of most things will be a web of supporting connections to the skin and air. 
Skins -  This controls how thick the outside layers are: 2 or 3 is general good. more skins will stiffen fine details while not increasing build times much.
Temperature - 220C - 240C works best for most things. To hot creates "sag"; to cold cause lack of layer adhesion.
Speed - This is a advanced setting that interacts with temperature. Slower can make "smoother" surfaces on curvey objects.

In most cases Required selections will make the difference between a build sucess and a build failure. Optimizing most of the settings will take a print from "ok" to "nice". 

Selection Action Advantages or  Better selection Disadvantages or poor selection
 Quality Required Med - faster, High - finer detail Med - low Detail, High - 3x more time 
 Raft Required Supports tall objects, fixes large flats leaves a rough bottom, post work
 Support Required Required for objects with overhang leaves a rough under hang, post work
 In fill Required Less is faster, lighter, and more flexible     More takes more build time , Less is fragile
 Skins Optimize More detail, stiffer structure                 Takes more build time, Less is fragile
 Temperature Optimize Hot - better layer adhesion too Hot = sag, too cold causes structure weakness
 Speed Optimize slower can use lower temperatures Takes more Build time, artifacts

Designs can be optimized for FDM and here are some videos on how to do that: Maker Faire 2013 Youtube talks