The standard technique is to use Text::xSV or Text::CSV. In this case it has to be Text::CSV because you are using an unusual quote character (!). Consider:

#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV;

my $csv  = Text::CSV->new ({quote_char => '!'});

print "Splitting data by comma as a delimiter \n";
while (<DATA>){
        next unless $csv->parse ($_);

        my @data = $csv->fields ();

        print "Data splitted is as below \n";
        print join("==>",@data),"\n";
        # i will do something else with splitted data in this iteratio
+n
}

__DATA__
!A001ST!,!98!,!1!,!01/10/1999!,!EUROPEENNE!,!0!,!EUR!,!6!,!7!,!0!,!98!
+,!1!
!A001ST!,!AD,CD!,!1!,!20/05/2004!,!ANDORRA!,!0!,!EUR,USD!,!6!,!7!,!0!,
+!AD!,!1!
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Prints:

Splitting data by comma as a delimiter 
Data splitted is as below 
A001ST==>98==>1==>01/10/1999==>EUROPEENNE==>0==>EUR==>6==>7==>0==>98==
+>1
Data splitted is as below 
A001ST==>AD,CD==>1==>20/05/2004==>ANDORRA==>0==>EUR,USD==>6==>7==>0==>
+AD==>1
[download]