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It can happen if all the points are at the exact same position (it may be the case in the file, or it's maybe because there's a reading error).

Can you send me the file maybe? (admin [at] cloudcompare.org)

Don't you use the 'Yes to all' button? Because in this case it only stops when it encounters large coordinates that cannot be 'fixed' with the previous Global shift values.

Or did I missed something?

Ok, this was definitely a bug. The 'interpolate SF(s)' check-box was automatically disabled when a SF was selected as 'layer' (so as to 'force' the user to select a projection strategy). But the fact that it was disabled was considered as a reason for not computing the scalar field! That's fixed in ...

Maybe because the file IS malformed? :p

Can you share it with us? (admin [at] cloudcompare.org)

Did you manage to find a reproducible way to 'achieve' this bug? (step by step)

Using a single number doesn't make sense when you have many points and distance values. The best you can say is exactly what appears at the top of the histogram: 0.003 average and 0.045 standard deviation (unless you have an excellent accuracy, I wouldn't use more digits - with 3 digits you''l get m...

I don't understand what you are trying to do or obtain with this 'average' values. The difference of the height averages is not directly linked to the average of the M3C2 distances... The M3C2 distance is more complex (it has in itself a kind of local averaging effect to be more robust to noise, but...

When you change the active layer, do you always press the 'Update grid' button?

Nope you can't export them currently (you would have to hack the code to do that). And I don't expect a big variability, as the ICP algorithm should more or less converge to the (almost) same position as long as the rough registration is not too bad. Mind also that with the default parameters of the...

So the average of the M3C2 will the difference in height which is around 0.003 mm? Sorry, I didn't understand your question. the thing which confuses me is the M3C2 contour maps showing a big difference but the number is small like 0.003 mm. What do you mean by "big difference" ? And if y...