Your comment is something I had noticed, but was unsure what to do about. I had been working on this for several hours with no luck and came for help, but somehow your comment triggered a different path. I got something that does exactly what I want it to, which is attached below. As a secondary thought, I want to be a better Perl programmer, thus if anybody has any ideas that are clear ways to do it better, or poor ways of programming in my code, I'm all for hearing them. Thanks!

$COMPFILE = IO::File->new;
$TMP = IO::File->new;
$COMPTMPLT= IO::File->new;

$COMPFILE->open("< comp_no_rods.txt" or die "Can't open");
$COMPTMPLT->open("< comp_template.txt" or die "Can't open comp_templat
+e");
$TMP->open("> tmpfile.txt" or die "Your TMP file sucks");

until ($COMPFILE -> eof){    
    $compline = $COMPFILE->getline();
    if ($compline !~ /END/){
        print $TMP "$compline";
    }
}    

$TMP->open(">> tmpfile.txt" or die "Your TMP file sucks");
until ($COMPTMPLT -> eof){    
    $tmpltline = $COMPTMPLT->getline();
    print $TMP "$tmpltline";
}
[download]