Taking out pages from PDF files, binding PDFs together, and removing PDF security. Here are a couple of free programmes to perform these tasks.

Taking out pages from a PDF

Sometimes PDFs contain a title page or blank pages that you might want to remove. PDFtk Server is a useful command line tool that can take pages out from a PDF file. To remove the title page from a PDF file, run the following command:

pdftk input.pdf cat 2-end output output.pdf

Set the pages you want to maintain within the document after the cat command, and change input.pdf and output.pdf to suit.

Merging PDF files

You may wish to combine a journal article with its supplementary information, or with comment letters and author responses. Again PDFtk can do this. To combine two pdf files into one:

pdftk input1.pdf input2.pdf cat output combined.pdf

PDFtk can also perform a host of other useful tasks - see its examples page.

Removing PDF Security

Sometimes PDF files come with encryption settings that prevent you from doing the above, or from performing OCR on the document. I find that QPDF works well for removing the security settings, even if you do not know the PDF password. To remove the security settings from a file run:

qpdf --decrypt input.pdf output.pdf

However QPDF does not always succeed. An alternative is to use a PDF printer driver to ‘print’ an unencrypted PDF. Examples of such software for Windows include CutePDF, Bullzip, PDFCreater etc. Preview on Mac will also ‘Export as PDF’. Ghostscript can also perform this task:

gs -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=output.pdf -c .setpdfwrite -f input.pdf

More Powerful Manipulation of PDFs

The python package pyPdf can be used to perform PDF file operations with the benefit of easy scripting ability. For instance when merging many hundreds of PDF sections of a larger document, each with a filename describing one part of the document (front matter, initial pages with Roman numerals, main pages…), I wrote a python script to merge the files in the correct order.

Edits

9^th June 2015 - Added ghostscript command to print to a new PDF file