I did something like this before, and I really like to split. This may or may not suit your needs, but it's the way I'd approach it without Parse::RecDescent (which I really like). It's your stuff firs, then mine.

#!/usr/bin/perl -wl
## note the -l flag
use strict;

## your stuff

my $string = q(
Outside.
{tag}
Inside level 1.
{tag}
Inside level 2.
{/tag}
Inside level 1.
{/tag}
Outside.
);

## original input
print $string;

while($string =~ s/\{tag\}(.+)\{\/tag\}/--Marked--\n$1\n--EndMarked--/
+gis)
{
    next;
}

## transformed output
print $string;

## my stuff
print "#" x 69;

my %tags = ( 'Tagged' => 'tag',
             'Bagged' => 'bag',
           ,);

$string = q(
Outside.
{tag}
Inside level 1.
{tag}
Inside level 2.
{bag}
bag level 1, inside tag level 2
{/bag}
{/tag}
Inside level 1.
{/tag}
Outside.
);

my $Sfactor = join '|', map {quotemeta} map {("{$_}","{/$_}")} values 
+%tags;

my @thing = split m/($Sfactor)/, $string;

for my $t(@thing)
{
    for my $tag(keys %tags)
    {
        $Sfactor = quotemeta "{$tags{$tag}}";
        $t =~ s/$Sfactor/--$tag--/;
        $Sfactor = "{/$tags{$tag}}";
        $t =~ s/$Sfactor/--End$tag--/;
    }
}

$string = join '', @thing; ## back as a string
print $string;
__END__
F:\dev\>perl markup.pl

Outside.
{tag}
Inside level 1.
{tag}
Inside level 2.
{/tag}
Inside level 1.
{/tag}
Outside.


Outside.
--Marked--

Inside level 1.
--Marked--

Inside level 2.

--EndMarked--
Inside level 1.

--EndMarked--
Outside.

#####################################################################

Outside.
--Tagged--
Inside level 1.
--Tagged--
Inside level 2.
--Bagged--
bag level 1, inside tag level 2
--EndBagged--
--EndTagged--
Inside level 1.
--EndTagged--
Outside.


F:\dev\>
[download]

 
___crazyinsomniac_______________________________________
Disclaimer: Don't blame. It came from inside the void
perl -e "$q=$_;map({chr unpack qq;H*;,$_}split(q;;,q*H*));print;$q/$q;"