If I understand your problem correctly, you want to collapse the '.' or ' ' guys that are between '|'. So how about using split and a map to break apart and rebuild your string?

while(<DATA>) {
        print;
        chomp;
        tr/\cM//d;
        my @x = split(/\|/,$_);
        my @y = map{($_ =~ /[\. ]/)?"":$_}@x;
        print join("|",@y) . "\n";
}
__DATA__
6|11-XXX-03|999999999|.| |0000|.|.|.|.|.|.| | |.| | | | |.|.| |.|0|N
[download]

This produces

6|11-XXX-03|999999999|||0000||||||||||||||||||0|N
[download]

when it runs.

Don't forget that split takes a regexp, not a quoted string. The "|" works out to (null)or(null), which means every position matches. Thus you get '|' between each character.

Final note: Don't always try to do everything with a regular expression. split and join are your friends.

--t. alex
Life is short: get busy!