What software or method, if any, can I use to perform optical
character recognition efficiently on multiple existing PDF files in
multiple file folders?  By way of clarification, I have thousands of
PDF files created by scanning on my hard drive, in hundreds of
folders.  The files are of typed documents, but are in graphical
format.  I have Abbyy Finereader, which is great OCR software, but in
order to perform the OCR I have to go folder by folder and select the
files, a process which would be too time consuming for all the files. 
I am looking for OCR software that I can simply point to multiple file
folders, and then have it automatically perform OCR on all of the
files in all of the folders and sub-folders, replacing the old files
with OCRd files of the same name.