If you want to export the PDF's you have several options.
You can download them from the user interface with the download file activity in a MF. You could even do a batch export with a Java action that zips a bunch of files and then downloads them.
When your application runs on premise you can export files to the file system of the server. For this you would again need a java action.
You could also use web services, you could for instance call a webservice from a document management system to drop the PDFS in there. Alternatively you could publish a web service that can be called by an external application to get the PDF files.
Another alternative would be a sftp server, in the appstore a module exists with which you can import and export files from a sftp server. Note that you will have to host the sftp server somewhere.
You need to use the Mendix entity System.FileDocument in order to determine which file is a pdf en which one is not based on the filename.
Or you could use a java action which determine the type based on the content
I mean to say here.When I generate pdf automatically it gets stored in this path.
But not in pdf format.
Its one of the requirement that they need all the pdf files generated out of mendix.