> The solutions I'm pursuing is this: use a macro to convert the spheres and
> cylinders in my scenes to meshes.  Then, there's a program called Poseray with
> will read my .pov files and convert them to objs.  But the .pov scenes have to
> be built from mesh objects.

The obj file format is very simple, if your spheres are cylinders are 
simple (ie there is no complex POV code/macro to generate the alignment) 
then it would almost be better to just write the obj file directly 
rather than creating the mesh in POV and the using Poseray.

> Where I'm stuck now is converting my scenes to meshes.  Could you recommend a
> macro to convert spheres and cylinders to meshes?

Others can help here, I usually "roll my own" for these type of things. 
It depends how much experience you have of 3D graphics, coding, etc, but 
it's not a huge task.

Another angle to attack from might be to use something like OpenSCAD. 
You can create spheres and cylinders with a similar syntax to POV, but 
in the end it will let you export the scene as a mesh (STL file in this 
case). Depending on how complex your POV scene is, it might just be an 
exerice with find/replace in notepad to get the scene to work in 
OpenSCAD and export a mesh.

Or does After Effects have an in-built scripting language you could use 
to generate the spheres and cylinders? Ditto above, you might be able to 
just use notepad to get the syntax correct for After Effects to use.

Do you also want different materials (colours) to be applied to each object?

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