It is not clear to me whether you want to generate your invoices from your FM database—and perhaps output them as pdf files—or merely retrieve data from files (pdf or otherwise) generated by some other means and then store that data in your file. Can you please clarify?
You can use the Monkey Bread Software plugin to OCR the PDF and then you can see if you can figure out patterns for pulling check numbers, amounts, dates, etc., from the OCR'd text of the check. It will be tricky since checks do not have a uniform layout with lots of text/char manipulations and tests.
MBS Plugin can do a lot here.
* extract PDF text
* render PDF pages as images
* extract images from PDF, e.g. with scans embedded in PDF.
* run image through OCR
but not sure what you exactly want.