How to separate out ProE data for Divestiture from Pro/INTRALINK 9.1?

How to separate out ProE data for Divestiture. We need to separate few hundred thousands of files for divestiture from Pro/INTRALINK 9.1. How do we achieve this without effecting other dependent files?

We have a list of files that needs to be seperated and we are working on Pro/INTRALINK 9.1 M060.

~Ash