OK, I got it to work now, maybe I did something wrong before, here is how I did it using boost threads and mutex
    bool update;
    boost::mutex updateModelMutex;
    pcl::PointCloud<pcl::PointXYZRGB>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZRGB>);
    void visualize()  
    {  
        // prepare visualizer named "viewer"
        while (!viewer->wasStopped ())
        {
            viewer->spinOnce (100);
            // Get lock on the boolean update and check if cloud was updated
            boost::mutex::scoped_lock updateLock(updateModelMutex);
            if(update)
            {
                if(!viewer->updatePointCloud(cloud, "sample cloud"))
                  viewer->addPointCloud(cloud, colorHandler, "sample cloud");
                update = false;
            }
            updateLock.unlock();
        }   
   }  
    int main()
    {
        //Start visualizer thread
        boost::thread workerThread(visualize); 
        while(notFinishedProcessing)
        {
           boost::mutex::scoped_lock updateLock(updateModelMutex);
          update = true;
          // do processing on cloud
           updateLock.unlock();
        }
        workerThread.join();  
    }
UPDATE:
According to this page The reason is that adding an empty point cloud to the visualizer causes things to go crazy so I edited the code above