Can I batch OCR?
Batch OCR
The latest version of PDFpenPro supports Batch OCR.
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Earlier Versions
If you are using an earlier version of PDFpen/PDFpenPro, there are ways to use AppleScript to batch OCR PDFs. The following articles provide some great examples:
https://talk.automators.fm/t/automatically-ocring-documents-with-hazel-and-pdfpen-pro/23
http://macsparky.com/blog/2009/5/24/pdfpen-ocr-folder-action-script.html