Open /dev/tty, and use that for user input.

#!/usr/bin/perl -w

use strict;

open(TTY,"+< /dev/tty")
  or die "Couldn't open tty: $!\n";
print TTY "Are you sure? ";
if (my $l = <TTY> !~ /^y/i)
{
  die "Cancelled by user.\n";
}

while (<>)
{
  print;
}
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