Hi !
Since the CityEngine creates models based on polygons, CityEngine was not designed to work with point clouds.
Thus what you'd need to do is use the tools ArcGIS provides to first convert the LIDAR data to (flat) shapes as a base for the footprints. I know there exists some tools like this, I just do not know them. This process may involve something like converting first to raster, then creating shapes from those raster files.
But once you have the shapes, you're good to go in CE.
I hope this helps further ..