This is a common thing. Various Linux tools do this all the time, so I'm not sure why the "standard" answer wasn't posted within minutes. /dev/tty is an alias for the controlling terminal:

while (<>) {
  $stream .= $_;
}

open TTY, "</dev/tty";
print "Do you want to process the stream?";
my $ans = <TTY>;
[download]

Alternatively, you can actually read from STDERR, just as you might print status or error messges to STDERR. If your reading inout from stdin, you might want to be able to write output to stdout too, rather than having your prompts go to stdout. You can print your prompts to STDERR or open the tty read/write "+</dev/tty".