Use Term::ReadKey.
The ReadKey function allows yout to specify a timeout. example (untested):

print "X done. Y starting in 15 seconds. Press any key to do Z instead
+.\n";
my $selection=ReadKey(15);
if ($selection)
{
     # Key pressed. Do Z.
}
else
{
    # No key pressed. Do Y.
}
[download]

Could easily be altered to use ReadKey(1) and print the prompt every second.