my %hash;
while (<file1>) {
  my $clean = ... convert $_ into its canonical form ...
  $hash{$clean} = 1;
}
while (<file2>) {
  my $clean = ... convert $_ into its canonical form ...
  if ($hash{$clean}) {
    # line from file2 exists in file1
  } else {
    # line from file2 is not in file1
  }
}