Hi George,
this is what I did with CS3 trying to recreate your question
1. created the pattern and filled the polygon shape
2. Object...Expand...(Fill only)...Ok
3. Outline... in the Pathfinder palette
4. Stroke with 1 point...just to get visibility
now, I didn't end up with closed shapes as in your image. All I have is open unfilled paths, being the pattern of lines and the segments of the polygon cutter path. The good news is that the cutter segments are all one next to the other at the top of the layers palette, followed by all the pattern lines.
5. Deselect everything
6. Select the first and last of the pattern lines and note their position in the layers palette
6A. to easily find their position go to layers palette menu and click on "locate object"
7. Select all pattern lines in the layers palette...

8. Collect in New Layer....in the Layers palette menu
9. Once the pattern lines are in its own layer, well the job is done

I hope it is of any help, this is my very first post!!! ....Still need a script to deal with hundreds of shapes?
CarlosCanto