Quality control of the prints

I'd like to control the quallity of 3d prints I make.
The idea is to get a 3d model of printed item and compare it to the sample.
By the sample I mean CAD or mesh model which was printed. Most of things I print was designed in Solidworks or 3ds Max, but recently we bought a desktop 3d scanner and started to copy things with it. I'd like to automate control as I 3d print parts which will be assembled for other people so the measurement is important.
The manufacturer says that this scanner can be used for quality control but I don't understand how and how to automate or semi-automate this process.