use CGI;
my $cgi = CGI->new( 'a.b.c=3&a.b.c=4&x.y=4' );

my $args = {};

my @names = $cgi->param;
foreach my $name (@names) {
    my $p = $args;
    my @keys = split /\./, $name;
    for my $i (0 .. $#keys-1) {
        $p = $p->{$keys[$i]} ||= {};
    }
    my @values = $cgi->param($name);
    $p->{$keys[-1]} = @values==1 ? $values[0] : \@values;
}

use Data::Dumper;
$Data::Dumper::Indent = 1;
print Dumper $args;