Like most things in law, the answers are going to come down to intent and outcome. If you distribute the PDF to other people with the intent that they can read the copyrighted works of an author, then you have distributed that author's content in violation of copyright. If on the other hand, you encrypted the entire contents of that PDF, threw away the encryption key and the published prints of the PDF as artwork of binary code, that's probably going to fall on the side of "fair use" even though the entire copyrighted work is input to and contained in your final output. Though you might get into some legal hot water if you promoted your work using the author's name, but that's more of a trademark issue than a copyright issue.