Meshlab alignment issue

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When I am trying to align two point clouds in meshlab, there is an error saying No successful arc among candidate Alignment arcs. And even though the point clouds after alignment can be seen in window, I cannot save it successfully. However I try, the ply file which I save always contains only the last layer, rather than all the layers. Dose the saving failure have something to do with the process error? How can I overcome this error? I work on Ubuntu 18.04 version.

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Meshlab will only export one layer when you export to any output file format. If you have several layers that should be exported to same file you need to merge the layer with the filter Flatten visible layer.

To run this filter you can click with the right mouse button on the layer list, or find it in the menu Filter->Mesh Layer->Flatten visible layer