#!/usr/bin/perl -w
use strict;

open(OLDF,"file.txt") || die $!;
open(NEWF,">newfile.txt") || die $!;

my $line=1;
while (<OLDF>) {
	s/^\s*(N\d+)?\s*/N$line /;
	print NEWF;
	$line++;
}
close(OLDF);
close(NEWF);