#!/usr/bin/perl
                
use strict;
use warnings;

my %HoH = (
        elt1 => {
                A      => "ccc",
                B      => "ccc",
                C      => "ccc",
        },
        elt2     => {
                A      => "ccc",
                C      => "ccc",
                D      => "ccc",
                B      => "ccc",
        },
        elt3    => {
                A      => "ccc",
                E      => "ccc",
                C      => "ccc",
        },
);

my %count;
my $count = keys %HoH;
while (my ($name, $hash) = each %HoH) {
    while (my ($key) = each %$hash) {
        $count{$key}++;
    }
}
while (my ($name, $hash) = each %HoH) {
    while (my ($key) = each %$hash) {
        delete $$hash{$key} unless $count{$key} == $count;
    }
}
use Data::Dumper;
print Dumper \%HoH; 

__END__
$VAR1 = {
          'elt2' => {
                      'A' => 'ccc',
                      'C' => 'ccc'
                    },
          'elt3' => {
                      'A' => 'ccc',
                      'C' => 'ccc'
                    },
          'elt1' => {
                      'A' => 'ccc',
                      'C' => 'ccc'
                    }
        };