Rules Based On PDF Annotations Or Markup

I have a bunch of scanned documents that for my use case there is handwritten information. I have been adding annotations/markup to the pdfs in Preview in an attempt make it machine readable for Hazel. It does not seem to be reading this.
Is there a condition I'm missing that would read this? Or does anyone have a free tool (CLI is fine) that I can use to burn in added information to a document in order to have Hazel process them?
Is there a condition I'm missing that would read this? Or does anyone have a free tool (CLI is fine) that I can use to burn in added information to a document in order to have Hazel process them?