The question is, however, how to use open3 in this case. You could supply different handles for the child's STDOUT and STDERR, but then it becomes very hard to communicate with the child. (You'd need to use IO::Select to avoid deadlocks.)

If you don't mind combining the child's STDOUT and STDERR into one stream, that's a much simpler option.

$pid = open3(
   my $to_child,   # Autovivified when false.
   my $fr_child,   # Autovivified when false.
   undef,          # Same as $fr_child when false.
   $somecommand,
   @args
);

...

waitpid($pid, 0);
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use Fcntl qw(:seek);

# save STDERR filehandle
open(my $ORIGSTDERR, ">&", STDERR);

# create temporary filehandle to catch STDERR
open(my $CATCHERR, "+>", undef) or die("cannot open temp file :: $!");
open(STDERR, ">&", $CATCHERR); # redirection


## STDERR is captured here ##
open(PIPE, '-|', $somecommand, $arg1, $arg2, $argN, $filename);

...


# restore STDERR filehandle
open(STDERR, ">&", $ORIGSTDERR);

# read captured STDERR from temporary filehandle
seek($CATCHERR, 0, SEEK_SET);
print "From CATCHERR: $_" while <$CATCHERR>;
close($CATCHERR);
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There are lots of CPAN modules to make this easier. If it's just a command you're running and you don't need to manage its STDIN, I'd use IO::CaptureOutput, which is my favorite swiss-army tool for capturing output either from Perl or from an external command. (So much my favorite that I took over maintainership when I needed bugs fixed and the author was non-responsive.)

use IO::CaptureOutput qw( qxx );

my ($stdout, $stderr) = qxx( $somecommand, @args, $filename );
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