I am looking for PDF re-formater that will cut all the (for me) unimportant information from the PDF such as headings, page numbers and possibly left/right padding.
Does anyone know about tool that could accomplish exactly that? Thank you for help.
You should find any PDF editor will enable you to cut or blank-out content.
Some of the editors will have batch processing capabilities, although identifying where a sub heading is positioned can be challenging.
An editor I use and recommend is Infix PDF editor from Iceni. This has a search and replace feature that can recognize text such as headings based on their font size and color.
Margin and other formatting information that may have been used by the originating application is generally lost when a PDF document is saved, so I'm doubtful it's possible to adjust padding.
It is difficult to do that easily. You could use pdftk to stamp each page but you need a white stamp that corresponds to the area to be blanked.