Section %N1%
  Sub-section %N2%

##</code><code>##

Section 1
  Sub-section 1
  Sub-section 2
  Sub-section 3

Section 2
  Sub-section 1
  Sub-section 2
  Sub-section 3

##</code><code>##

#!/usr/bin/perl
my ($file,$n1,$n2,$tpl);

$file	= shift;
$n1		= shift;
$n2		= shift;

open(F,'<',$file) || die;
while(<F>){ $tpl .= $_; }
close(F);

if ($n2){
	for($i1=1;$i1<=$n1;$i1++){
		for($i2=1;$i2<=$n2;$i2++){
			$str = $tpl;
			$str =~ s/%N1%/$i1/gi;
			$str =~ s/%N2%/$i2/gi;
			print $str;
		}
	}
}
elsif($n1){
	for($i1=1;$i1<=$n1;$i1++){
		$str = $tpl;
		$str =~ s/%N1%/$i1/gi;
		print $str;
	}
}

##</code><code>##

./script.pl templatefile 2 3