Enter PdfMasher. PdfMasher asks the user about the role of each piece of text, and does it in an efficient manner. Your PDF has a header on each page and you don't want them to litter your text? Sort text elements by Y-position (thus grouping them all together), shift select the elements and flag them as ignored. They will not appear on your final HTML. Your PDF has footnotes on many pages? Sort your elements by text content (thus grouping all elements with the text starting with a number together) and flag them as footnotes. They will be moved to the end of the document, and PdfMasher will try to create hyperlinks to footnote references.
Install PdfMasher on ubuntu 11.04 (Natty)
Download deb package from here once you have deb package you can install by double clicking on it.
PdfMasher Demo Video