Formatting PDFs using Adobe Acrobat
PDF files need to be "tagged" in order to be considered accessible. To tag a PDF, use Adobe Acrobat. WebAIM provides step by step instructions on editing Acrobat files for accessibility.
The National Center on Disability and Access to Education (NCDAE) also provides a helpful guide that includes a video. They note, "It is easier/better to make documents accessible as they are created."
Sources: NCDAE: Creating Accessible PDF Documents In Adobe Acrobat XI and WebAIM: Acrobat and Accessibility