Greetings all,
Okay This is only an idea based on some of the things I have seen elsewhere... again this is just an thought.
Could you in your perl script open a filehandle to a run of your C program?
Something similar to :

open (MAIL, "| /usr/sbin/sendmail -t") || die "no mail for you!";
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but instead of sendmail it would be your C program

open (CPROG, "| /path/to/your/program") || die;
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then pipe all the filenames to the filehandle you created?
or am I way off here?
Just a thought...
-injunjoel