In case it helps, I developed a little bash script to automate OCRing a PDF PRIOR to placing it into EagleFiler. I'm sure you can modify it to suit your needs AFTER the file has been imported into EagleFiler. Sadly, ABBYY FineReader (I'm running version 4.1) is not directly scriptable (it does not support AppleScript).
Code:
#! /bin/bash
# First test to see if the document has already been OCR'd
if ! grep Font "$1"
then
# Open ABBYY and start to OCR the PDF
open -a 'Scan to Searchable PDF.app' "$1"
# Wait for the completed file to appear in the Finder
while [ ! -e "${1%.pdf} processed by FineReader.pdf" ]; do
sleep 5
done
sleep 5
# Remove " processed by FineReader" from the file's name
mv -f "${1%.pdf} processed by FineReader.pdf" "$1"
# Tell Finder to hide ABBYY FineReader using Applescript
osascript -e 'tell application "System Events" to set visible of process "Scan to Searchable PDF" to false'
fi
If the PDF did not originate from your ScanSnap, ABBYY FineReader will not be able to OCR it; the "Creator" of the PDF needs to be "ScanSnap Manager". You'll need to perform an additional trick upfront if you'd like to OCR PDFs that did not originate from your ScanSnap. Let me know if you'd like to know how that's done.