Hmm...sorry, if I haven't been clear. The die lines are not the issue. We want to keep only the die lines and registration marks (black circles in screenshots). I don't have an issue isolating those things with spot colors.
The problem I am having is targetting the transparent objects and clipping masks. I can't find a way to target those things to remove them.
Even though I can get all the spots on to a layer, I cannot get the objects mentioned above to be removed from the PDF.
Can you post the problem pdf file so we can review and test it ourselves? Might also be good to see the original file before imposition to understand where the file is starting from.
If you have the Advanced Pre-Press license, the Optimize node's ability to remove transparent objects might be worth trying.
So unzip the attached workflow then try importing. The workflow uses a couple of the already shared preflight fixups (remove layers) I made them specific to your files layer names. Also added the "remove all pdf boxes" fixup.
Not all the things you need (like the registration marks etc) but maybe test your file through the workflow and see what you think. I also attached the output I got. You might not need all the items I did - but hey, kept swinging at it until it looks like what you asked for.
You will not (I dont think) be able to remove the last remaining boxes that appear with the select all in illustrator because those are the object (dpart)? boxes. There might be a way to change them but that is probably way more work!
By the way, I used a quick test file I generated in illustrator (just a vector shape) with no clipping paths or layers etc. The small file imposed and shows the same boxes you see in illustrator after imposition. My understanding is that the imposition is done in a way to optimize files - the size of the file does not grow because the artwork is typically embedded once and 'linked' or 'referenced' for the step and repeat process of placement on the page. I believe the blue boxes that are left represent those links/placement. Havent found anything to describe what to even look for to 'merge', 'remove', 'delete', or anything else for these boxes.
So the flattening and clipping path removal didnt take it any further in my testing. However, I agree and concur that re-distilling with Acrobat Distiller DOES remove the last set of boxes. I did some initial testing with Ghostscript to conver the PDF to PS and then convert the PS back to PDF. It retains the boxes. The PS file out of Ghostscript Distilled with Adobe Distiller again, does remove the boxes.
Have to see if there are any other options in GhostScript that might more accurately mirror what Distiller is doing.