I suggest against this heterogeneic approach. STL files do not explicitly contain information about the coordinate system, so depending on the method of saving the file in your chosen application, they may appear on top of each other. In either case (appear correctly vs need to manually align) you can convert the STL models easily into 3D volumes (i.e. labelmaps) in the Segmentations module (you can find lots of information about this in the documentation and this forum).
Once you have the labelmap you will need the exporter above so that you have the desired binary file format.