use strict;
use warnings;

use Data::Dumper;

my $h =
{
    a => { c=>"b" },
    A => { C=>"B" },
};

delete $h->{a}{c};
delete $h->{A};

print Dumper ($h);
[download]

prints

$VAR1 = {
          'a' => {}
        };
[download]

as expected. You might want to show us some of your code.