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Yes, you should be able to do this with pcl registration. Check out the tutorial for ICP registration: http://pointclouds.org/documentation/tutorials/iterative_closest_point.php

I think the best initial approach would be to keep a downsampled combined pointcloud, and use ICP to register new clouds to the existing cloud, then add the new points to the combined cloud. Afterwards, you can use clustering ( http://pointclouds.org/documentation/tutorials/cluster_extraction.php ) to separate the objects out.