Convert a 3D NumPy array of voxels to an STL file
I agree with the use of OpenSCAD, but since it is difficult to program in OpenSCAD, I would use SolidPython, which is a front end for OpenSCAD with the full programming capability of Python.

In the alternative, you could use any programming language to decode your arrays and generate the OpenSCAD code for the little network of cubes (or voxels).

The final possibility is to generate an STL file directly.  I've helped someone do this, but we found the rules to be a little non-intuitive.  We used mesh tools to check out results, both by looking for error messages, and by displaying the result to see if it looked as we intended it to look.