I have had a lot of experience in alignment of scans to many different objects. Such as a part scan to a model or a part scan to a check fixture.
To truly answer your question I would know what it is you are trying to align. Usually we prefer to data collect our 3d scan with the same cmm that we collect the 2d with. If that is not an option then we will use features that can be scanned and data collected. If that is not possible we will attach a 1-2-3 block to the item and use it for alignment.
There are some software programs that are able to do a best fit alignment of a 3d scan to a 3d cad model, such as Polyworks 2016-IMInspect.
Feel free to pm me for more info and a better explanation.