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In the general case, it is an impossible task for software. A PDO file includes a lot of information, like edge connectivity and 3D topology, which simply isn't described in your random PDF. On the other hand, a 2D file is likely to contain metadata, such as instructions, borders and titles, which have no PDO counterparts - how could the application know what is to be discarded?
Any such software would need a lot of manual help (read: knowledge about the finished model). Even detecting if the PDF actually represents an actual 3D object is complicated.
Now, if you know the PDF is a special case - say, it was actually generated from an original PDO using a known version of a specific software, like a virtual printer, and using Pepakura's "smooth lines" option and few or no extraneous data like instructions had been added, the task is much easier, but still complex, and the software likely wouldn't be completely automated - only it'd be able to ask for help more intelligently.
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