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How aligned, and what are your constraints on the output? That really makes a big difference.

If you're willing to lose some representational accuracy, you can run the concatenated cloud through a VoxelGrid filter, which downsamples the cloud and leaves only one point for every x^3 size cube (leaf). This is essentially what the octomap will do, except that the output remains a point cloud.

If every point is perfectly aligned with every other, which is extremely unlikely, you can insert all the points into a (Map)[http://www.cplusplus.com/reference/map/map/], using the x,y,z tuple as the key, and remove any points that double up on one key.

How aligned, and what are your constraints on the output? That really makes a big difference.

If you're willing to lose some representational accuracy, you can run the concatenated cloud through a VoxelGrid filter, which downsamples the cloud and leaves only one point for every x^3 size cube (leaf). This is essentially what the octomap will do, except that the output remains a point cloud.

If every point is perfectly aligned with every other, which is extremely unlikely, you can insert all the points into a (Map)[http://www.cplusplus.com/reference/map/map/], Map, using the x,y,z tuple as the key, and remove any points that double up on one key.