I use a program called CamBam to generate a gcode file and then load that into Mach 3 which is what actually controls the engraver. In the videos below I'm using a model purchased from VectorArt3d called Mountains and Forest, pulled it into CamBam, set the depths, size, bit size, etc. If I were doing text or a logo I'd go through the same process. The actual engraving for a 3D model is a lot more involved than straight text or shapes (which is why its expensive).
For the first pass I use a 2mm bit in 'waterfall mode' this means it calculates how much material it can take off by following the contours (as opposed to scanning back and forth). In the video above it has finished the waterfall and is starting on the second pass (1mm bit, very little overlap).
Here we're starting the third pass with a .5mm bit horizontally this time.
and here we're getting towards the end. I then go over it with a polishing wheel on a dremel to take out any remaining scan lines and refinish to match the rest of the case.