Could you please use following steps to create or display the xyz data in a 3D way?
1. Add the XYZ in ArcMap.
2. Right click on the file > Display XY. It will create a point event layer
3. Export the event layer to create a feature class or shapre file.
4. Go to Spatial analyst tool bar > Interpolation > Topo to Raster. It will create a surface.
5. Add this raster in ArcScene or use it in raster calculator for any 3D calculations.
I hope this is helpful.
Please let me know if my understanding is wrong.