How do I distinguish the header/footer from the two-colume format of a .pdf document?

How do I get adobe to realize that there is a header and footer on each page, but the actual text in the file is in two columes. Is there a way to make this clear and embade it in the document so other programs recognize this too?
I am finding tha when I copy/paset text from this .pdf document the pasted text combines thet text across each line especially when images are involved in the selected feild. This 600 page document is formated into two columnes but has headers and footers and inserted articles and pictures that obscure fields. Here isinimage of what I mean.

Scripts can be placed in many different locations, but in this case an Action is the right choice since you want to process multiple files in the same manner.
You can set the output option of the Action to "Do not save changes", since you're already taking care of that in the script and don't actually need to save the original files.
It seems to me the script is doing what you want it to do, no? It creates the PDF files from the extract pages of each source file.
All you have to do now is to combine all of these files together, which you can do by going to File - Create - Combine Files into a Single PDF and select the folder to which you saved all of these files.

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