If a PDF has not undergone Optical Character Recognition (OCR), then it cannot be highlighted with the standard iAnnotate Highlighter. The Highlighter is a text markup tool that does not work with files that haven not undergone OCR, since these files are images and not textual documents.

Documents can undergo OCR via a desktop application such as Adobe Acrobat. In lieu of such OCR methods, you may wish to use the Freehand Highlighter to annotate your PDFs.