Waterjet quoting and final cutting is driven from 2D vector format files. However, many people use 3D modeling tools for their designs. Popular software packages in this category include Pro/Engineer, Sketchup, SolidWorks, Inventor, Geomagic (Alibre) Generating an appropriate 2D file generally means going though an export process to get the correct projected version of the parts to be made.
The biggest stumbling block here is that many 3D design tools will add perspective information, such as hidden lines, to the final output. Lines in the drawing to indicate perspective simply confuse the waterjet software. Below is an example of this problem. The original design was exported as a 2D drawing from ViaCAD (though this problem is by no means unique to that package. When zoomed out, the part looks like a simple outline.
However, when you zoom in on the upper right hand corner of the image, you can see that the software has drawn the front and back of the part in perspective, plus a middle line. The extra lines will simply confuse the waterjet software, as there is no real indication which line represents the outline to cut.