title_body: How to convert PDF's with footnotes for Kindle? I have a collection of PDF files which I'm looking to load onto a Kindle.  First, however, they need to be converted.
  Experimentation gives sub-par results by selecting and converting to mobi through calibre.  Better results are achieved by copy/paste to a text file.  I haven't yet tried a bulk convert to text from calibre.
  Some PDF's have very odd results, where what's visually and logically a paragraph of text is somehow &quot;columns&quot; either when copy/pasted or converted.  The result is a sort of interlace, but slightly out of sequence.  However, that's unusual.  For the most part/copy past gives excellent results.
  These PDF's generally are all text, with footnotes.
  It's a bit mystifying why copy/paste would be better than calibre converting to mobi.
upvoted_answer: PDFs are not designed to be converted from. They have no structure that allows Calibre to determine for sure how many columns of text it has or what's a footnote. The Calibre manual describes the topic in more depth.
  I found that copying the text to a text editor, cleaning it up and then pasting it into the Calibre e-book editor gives the best results but it takes long and is boring.  I've written down my work-flow in a blog post. It describes how to make EPUBs, but I'm sure it can be adapted to mobi fairly easily, since it seems to use XHTML too.