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Short answer, yes. sensor_msgs/PointCloud2 is the message type to transmit point clouds; if you want to do pcl processing with them you'll need to convert them to pcl::PointCloud<T> using pcl::fromROSMsg and pcl::toROSMsg.

For the long answer, see the ROS/PCL overview and the tutorial. As indicated on the latter:

The sensor_msgs/PointCloud2 format was designed as a ROS message, and is the preferred choice for ROS applications.

The pcl/PointCloud<T> format represents the internal PCL point cloud format. For modularity and efficiency reasons, the format is templated on the point type, and PCL provides a list of templated common types which are SSE aligned.

Hope it helps!