Hi Par_Navidi,
In QuantumATK, you are able to build and import your own monomers into the Monomer Database. In this case you can build a monomer of kapton in the builder. Remember to tag the head and tail atoms so that the Polymer Builder knows how to connect the monomers to form a chain. Using the imported monomer you should be able to use the Polymer Builder to create a 3D amorphous structure of kapton. If your material is crystalline and you know the crystal structure, you can also import CIF files into the Builder.
With respect to the thin film part of your problem, the Polymer Builder packs polymer chains into the simulation cell with isotropic orientations. It currently doesn't support aligning the polymer chains along a particular axis. On the scale of atomic simulation 20nm is quite large, so it may be necessary to consider the material as continuous in all directions and then apply stress in particular directions.
Cheers,
Brad.