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In case someone finds this useful, here is how I solved it:

Convert the sensor msg to a PointCloud<pointxyz>, this removes all fields except xyz, then convert back to a sensor msg.

An example:

  sensor_msgs::PointCloud2 msg; // contains x,y,z and other fields such as intensity
  pcl::PointCloud<pcl::PointXYZ> tmp;
  pcl::fromROSMsg( msg, tmp );
  // Here you could perform operations on the point cloud
  pcl::toROSMsg( tmp, msg );