If all you want to do is capture all lines that aren't blank and don't containt POLYMORPH, then just tell perl to do that:

my @data;
while( <IN> ) {
    chomp;
    push @data, $_ unless /^\s*$/ or /^POLYMORPH/;
}
[download]

Using Data::Dumper this gave me:

$VAR1 = [
          'C 1, 1( 9)',
          'C 2, 2(11)',
          'R 2, 2(18)',
          'C 1, 1( 4)',
          'C 2, 2(18)',
          'C 1, 1( 4)',
          'R 2, 2(18)',
          'C 1, 1( 9)',
          'C 2, 2(18)',
          'C 1, 1( 9)',
          'R 2, 2( 8)',
          'C 1, 1( 0)',
          'C 1, 1( 0)',
          'C 1, 1( 9)',
          'C 2, 2(18)'
        ];
[download]

You may want something more complex than that...

--
"To err is human, but to really foul things up you need a computer." --Paul Ehrlich