How to extract data from a PDF file while keeping track of its structure?

There is essentially not an easy cut-and-paste solution because PDF isn't really very interested in structure. There are many other answers on this site that will tell you things in much more detail, but this one should give you the main points:

If identifying text structure in PDF documents is so difficult, how do PDF readers do it so well?

If you want to do this in PDF itself (where you would have the majority of control over the process), you'll have to loop over all text on pages and identify headers by looking at their text properties (fonts used, size relative to the other text on the page, etc...).

On top of that you'll also have to identify paragraphs by looking at the positioning of text fragments, white space on the page, closeness of certain letters, words and lines... PDF by itself doesn't even have a concept for a "word", let alone "lines" or "paragraphs".

To complicate things even more, the way text is drawn on the page (and thus the order in which it appears in the PDF file itself) doesn't even have to be the proper reading order (or what us humans would consider to be proper reading order).

PDF parsing for headers and its sub contents are really very difficult (It doesn't mean its impossible ) as PDF comes in various formats. But I recently encountered with tool named GROBID which can helps in this scenario. I know it's not perfect but if we provide proper training it can accomplish our goals.

Grobid available as a opensource on github.

https://github.com/kermitt2/grobid

You may do use the following approach like this with iTextSharp or other open source libraries:

• Read PDF file with with iTextSharp or similar open source tools and collect all text objects into an array (or convert PDF to HTML using the tool like pdftohtml and then parse HTML)
• Sort all text objects by coordinates so you will have them all together
• Then iterate through objects and check the distance between them to see if 2 or more objects can be merged into one paragraph or not

Or you may use the commercial tool like ByteScout PDF Extractor SDK that is capable of doing exactly this:

• extract text and images along with analyzing the layout of the text
• XML or CSV where text objects are merged or splitted into paragraphs inside a virtual layout grid
• access objects via special API that makes it possible to address each object via its "virtual" row and column index disregarding how it is stored inside the original PDF.

Disclaimer: I am affiliated with ByteScout