distance point cloud and partial point cloud

[Kameelpeerd]

Hi,
I have 2 point clouds: 1 of an object, the other of only part of that object (with different noise), say 1 large square with a hole near the side and 1 small square with a hole. I want to:
- auto-align (finely register) the smaller point cloud to the larger one (after rough alignment)
- calculate the difference (distance) of the two.
The problem is, that apparently not only the distance from the smaller cloud to the larger cloud is calculated, but also the distance of the remaining points of the larger cloud to the smaller cloud. This means, that in case of the squares the smaller square always is centered on the larger one, because that minimises the cumulative squared distances of the edge points of the larger square to the smaller square.
My question: is there a way to only include the distances from the points of the smaller cloud to the nearest points of the larger cloud?

[daniel]

Have you set the 'Overlap' parameter correctly? I mean less than 100%?

[Kameelpeerd]

ahh... that's it, combined with setting the reference correctly :)
Sorry, I am new to this and took a wrong turn somewhere. Now I understand!
Thanks very much!