Forrest Higgs posted about a script he had written to flip an STL.

Stupid question for anyone who owns a MakerBot – would flipping one of the X or Y stage motor cables (or perhaps flipping the axis in RepG) serve to flip the STL without the need for writing new scripts?

Edit:  Well, there you have it.  Andrew Plumb/Clothbot agrees.  Flipping the X/Y axis will flip your object\.  No STL fiddly scripts necessary for MakerBot owners!