Q: How do I differentiate footnote and bibliography from the actual
text in the pdf?
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A: Unless your PDF is tagged, or it constants logical structure (which
can be accessed as shown in LogicalStructure sample
http://www.pdftron.com/pdfnet/samplecode.html#LogicalStructure) there
is no simple way to differentiate between logical groups in PDF
documents. In this case you may need to use text positioning
information and other layout and styling cues (e.g. as returned from
'pdftron.PDF.TextExtractor', TextExtract sample) to infer that a given
text block is a header, figure, a title, or something else.