Save this file as main.tex
\documentclass{article}
\usepackage{hyperref}
\begin{document}
\section{Document 1}
\pdfbookmark[0]{file:file1}{file:file1}
This is Document 1
\newpage
\section{Document 2}
\pdfbookmark[0]{file:file2}{file:file2}
This is Document 2
\newpage
\section{End of Document}
\pdfbookmark[0]{file:bogus}{file:bogus}
This is necessary to avoid a bug. The program fails to create the last document.
\end{document}Run pdf-splitter:
$ pdflatex main.tex
$ mkdir out
$ pdf-splitter main.pdf out/
$ ls out/
file1.pdf file2.pdfEnsure that each \pdfbookmark is on a new page. If you use \chapter, that takes care of it.