'abcdef' =~ / ( abc ( def) ) /x;
   $1 -> 'abcdef'
   $2 -> 'def'
[download]

So you have two options here. You can either specify each matching group, or match in a loop. For instance:

    use Data::Dumper;
    my $table_ref="!Frequency[A][B][C]  ..some other text..";


    ### Groups specified explicitly

    my $var_rx   = qr / \[ ( [^\]]+ ) \] /x;
    my $file_rx  = qr / ! ( [^\[]+ ) /x;
    my $regex    = qr/^ $file_rx $var_rx $var_rx? $var_rx? $var_rx? \s
++.*/x;
 
    my @matches  = ( $table_ref =~ /$regex/);
    print Dumper (\@matches);    

    ## Loop
    my ($filename) = ($table_ref =~ /^ $file_rx /gcx );

    my @vars;
    while ( $table_ref =~ /\G $var_rx/gcx ) {
        push @vars,$1;
    }

    print Dumper($filename,\@vars);
[download]

See perlre for an explanation of \G and /c

clint