Trina,
So to the best of my knowledge, you'll need to do that outside of Eloqua as you cannot apply filters of any kind to unmapped data cards. I'd recommend you upload the data set, see what maps and what doesn't via the Data Card reporting option "Data Cards Mapped to Contact Breakdown" (located in the top right corner of the Data Card Set frame). In the report, there is a row that includes a total for all unmapped contacts which you can select and then export that file from Eloqua for further review.
As far as the data cards mapped to contacts, you can segment/filter on those via a Segment - select Filter Criteria, Has Linked Record in Custom Object, select the Custom Object and then click "add" to see field options with applicable operators.
I hope this helps!
Best,
Kristin