In 'Legacy', it is clearly depicted that Humans [Users] when injured in the digital world, bleed what resembles blood -- instead of simply derezzing as the native programs do. This suggests the internal organs of Users are at least structurally reminiscent of their anatomy from the real world.
Quora is depicted, as having a digital DNA in her resuscitation/repair scene, which presumably is what marks her (and the ISO's) as being inherently different from the other programs.
This leads me to hypothesise that she is genetically prepared to survive digital manifestation through portal to the physical world. Which is why Flynn (the Elder) is so incredibly excited about the discovery of the ISO's
Does that mean she would bleed little fluorescent blue cubes in the real world?
I can't say, but I would hypothesise her internal structure in the real world would be akin to her digital self -- and vastly different from our own.
"Biomechanical Jazz" as Kevin Flynn puts it.
This brings up the question whether a Regular Program could be materialized in the real world.
CLU clearly thinks so -- because his whole world-domination plan hinges on the ability to bring an army of programs through the portal.
However it is never demonstrated in either of the films whether it is possible for a regular program to be materialized.