STL files can be a nightmare to work with in traditional CAD packages because the model consists of faceted faces. Manipulation/orientation is difficult to say the least.
At 3D Scanning Solutions not only do we have the ability to re-orientate the STL/OBJ/STEP part/assembly we can also create datum planes in alignment with key surfaces, cylinder etc.
We are also able to fill in holes to make the part watertight which also means packages such as CREO/Solidworks will be able to convert them into a solid model.
At present our deviation checks are carried out in Geomagic Control & reports can be created in any program but at present we tend to use powerpoint.