Sonia, it can be done by exporting 2 gedcom files and importing them into separate new PAF data files. Or it can be done by using File > Save As, and then selecting and deleting the lines you don't want in the file. As always, make a backup BEFORE any major changes so you can always get back to where you are in case something goes wrong.
But after years of keeping my genealogy and my wife's in separate files I found it more practical to have us all in one file. Where there are children and grandchildren it gets awkward trying to update both files and keep them in synch. I understand that if the file gets really large, PAF slows down. I have talked with people who have 50,000 records and they have said it is not a problem.