Another thing yo could try, is doing some pipe magic: open a pipe, reopen STDERR to the write end of the pipe and have your filter read from the read end:

pipe (STDERR_READER, STDERR_WRITER) or die "Pipes clogged: $!\n";
close STDERR;
open STDERR, ">&STDERR_WRITER" or die "Could not dup STDERR: $!\n";

sub my_output_filter {

  my $line=<STDERR_READER>;
  do_something_funny_and_possibly_even_useful;

}
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CU
Robartes-