To align manualy you need at least 2 scans. set the first one as "Reference" and secend one as "Aligned". I think this is a bug. it should be NOT Aligned.
Select Manual Alignment. click on Create Marker Pair.
Right click on a surface or edge that is reprecented on both scans. Now you have one pair of points. Do this on 3 different surfaces and then click on Align. now you have to select if alignment was successful or not by clicking Apply or Reset.
If you get a bad alignment, try again.
I hope this will help you out.
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RE: How to use CR Studio Manual alignment.