You could do this:

while(<fp>)
{
  s/\(/\n\(\n/g;
  s/\)/\n\)\n/g;

  my $line = join "\n",
             map { # do stuff to individual line at $_ }
             split /\n/, $_;
  # save line to array, possibly?
}
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Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain