#!/usr/local/bin/perl -w
use strict;
my $pattern = quotemeta( "|" ) . '?[ *|\.*]' . quotemeta( "|" ); 

while(<DATA>) {
        print;
        chomp;
        s/\cM//g;
        s/$pattern/\|\|/g;
        print "$_\n"; 
}
__DATA__
6|11-XXX-03|999999999|.| |0000|.|.|.|.|.|.| | |.| | | | |.|.| |.|0|N