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.
Are you looking to do this While the part is being printed or when it is finished?

I imagine you would need some kind of Algorithm that scans the part and compares it to the original. You may need to add something to the scan for the program to get a calibration measurement off of. Not to mention build a device that allows the camera to be rotated around the part via automation to do your scan. I strongly believe that this is a good idea as it would give the camera a steady scanning speed and set distance to the part. For calibration measurements you can easily place cubes or squares in the backdrop a specified distance apart and program that numerical calibration into the Algorithm.

I am probably grossly over thinking this, but I like to over engineer first then simplify as I see that I can.