Which 3D design softwares make multi-material amf or other design files that slic3r will slice?
A Scriptable Process for Generating Multi-Material STL Files:

I am now using interactive CAD software to define the more complex features of the object I am printing (in the current case, clock faces), and then using OpenSCAD to do the boolean volume operations.  

To print the composite object, I need three STL files, one for each material I am using.  The three parts are the clock body, the translucent optics to conduct the LED lights, and the clock numbers.  

I need:


one STL for the body minus the LED optics and minus the numbers.
one STL for the numbers minus the LED optics, and
one STL for the LED optics.


The CAD package supports the operations, but every time I change anything, I have to jump through several hoops to combine the three parts, manually and recreate the three objects.  

I had used OpenSCAD to make the optics and the numbers, and they were never in the same coordinate system as the clock body from the interactive CAD package.

So, I scripted it and used OpenSCAD to read the clock body STL and being it into OpenScad.  I transformed it into the common coordinate system.  I then did, one by one, based on a command-line parameter, the boolean operations, rendered the result, and exported the resulting STL file.

When I read the three files into PrusaSlicer, the lined up perfectly and everything worked simply, without and precision hand-eye coordination, and with no drama.

Scripts and command lines work for repeatability far better than squint, drag, and guess.