Yes, splitting is the simple solution.

sub get_groups {
    my @groups = ();
    my $level  = 0;
    my $group  = "";

    #Keep on increasing the level once you find the opening brace.
    #After coming out of loop, level should be again 0

    foreach my $val ( split //, shift ) {
        next if $val =~/\s/;
        if ( $level == 0 && !($val ~~ [ "(", ")" ]) ) { push @groups, 
+$val; next; }
        if ( $level != 0 && !($val ~~ [ "(", ")" ]) ) { $group.=$val; 
+next; }

        if ( $val eq "(" && $level==0) { $level++;$group = ""; next; }
        if ( $val eq "(" && $level!=0) { $level++;$group .= "("; next;
+ }

        if ( $val eq ")" && $level==1) {$level--;push @groups, $group;
+ $group = ""; next; }
        if ( $val eq ")" && $level!=1) {$level--;$group .= ")"; next; 
+}
    }

    print Dumper(@groups);

} ## ---------- end sub get_groups
[download]

Input:

my $string = "A (B C D)";
get_groups($string);
$string = "A (B C D) (E F G)";
get_groups($string);

$string = "A B (C (D E) (F G)) (H I)";
$string = "(A B) M N ((C (D E)) (F G)) (Z(H I)) T R";
get_groups($string);
[download]

Output: $VAR1 = 'A'; $VAR2 = 'BCD'; $VAR1 = 'A'; $VAR2 = 'BCD'; $VAR3 = 'EFG'; $VAR1 = 'AB'; $VAR2 = 'M'; $VAR3 = 'N'; $VAR4 = '(C(DE))(FG)'; $VAR5 = 'Z(HI)'; $VAR6 = 'T'; $VAR7 = 'R';