I use mupdf-tools' pdfclean command for that. pdfclean -d in.pdf out.pdf However qpdf seems to have more features. The most interesting for me: The QPDF l

I use mupdf-tools' pdfclean command for that. pdfclean -d in.pdf out.pdf However qpdf seems to have more features. The most interesting for me: The QPDF library also makes it possible for you to create PDF files from scratch. In this mode, you are responsible for supplying all the contents of the file, while the QPDF library takes care off all the syntactical representation of the objects, creation of cross references tables and, if you use them, object streams, encryption, linearization, and other syntactic details.