We miss an alternative of Make Feature Layer tool for 3D data. If we want to convert many 3D shapefiles into multipatches, there is no automatic way to do this because Make Feature Layer tool does not recognize 3D data. Therefore Layer 3D to Feature Class is useless in ModelBuilder. The only way is to add few (memory limits) 3D shapefiles to ArcScene and run batch Layer 3D to Feature Class manually. Very time consuming at the moment.