The manual alignment will only work well if you haven't scanned too much data, and if the points you select are really close to being the same points on the part. The software will try to match the clouds as long as you get them close enough.

Here is a hint in regards to scanning larger objects: Pan your scanner rather than rotate it around the part if you are trying to get aligned shots of a side of your part. This way the overlapping area will be from the same angle and more of the data will be the same. Once you have the entire side scanned this way, then turn the scanner to take the side from a new angle. This greatly reduces the chances of misalignment.

In most cases if the scanned data isn't automatically aligning, it is better to take another scan with more overlap than to try to align the one you took. The EinScan-S software is pretty good at finding where your scanned data should go, though there are times I still resort to alignment manually.

Overall, the key to getting good scans is to try not to get too much overlapping data as a whole. I know that sounds counter-intuitive, because alignment requires overlapping data, but the more scans you have, the more you will have errors stacking up, not too mention as you get a bunch of data you will start to risk crashing. I have built reference surfaces covered in black with only a few distinct registration features that are light colored so when I scan a large part it can find those features and lock in alignment so I don't have to worry about having massive amounts of scan data to have accurate alignment. I'm scanning parts well beyond the size and complexity that Shining 3D intended (They have told me as much as few times) so I have had to become creative. This is one of the main reasons I think higher quality scanners use registration markers.

I am working with them to improve the software to tackle larger and more complex objects. They are working hard toward making this software better for everyone so have faith that buying this scanner is a good investment, it is getting the software improved as we go along.

Dave @ Nerv