Hello, you are going to have to give us a bit more information if we are going to be able to help you:

• What have you tried? Code? Data? Error messages ( Always use strict and warnings )?
• What do your hashes look like (try printing them out with Data::Dumper) or what do yout *think/want* they/them to look like? The way you have written them out gives us no clue as to how they are structured! You can use < code >< \code > tags to preserve formatting (indentation etc... see Markup in the Monastery) if you prefer to write it out that way.
• How do you want to compare them? Keys? Values? Both? Memory location? Structural equivalence? etc...
• Maybe check out Data::Compare...

That's the point, i cant seem to figure out how should i structure them. i dont know too well how to use hashes of hashes. i want to write code which reports all the differences between the two libraries. the 1st hash should be iterated and check its existence in hash 2 and then vice versa.

use strict;
use warnings;
use Data::Comparator qw(data_comparator);
use Data::Dumper;

my $file1 = <<EOF;
Cell: AND1
A1 A2 Y
Cell: INV1
A Z
EOF

my $file2 = <<EOF;
Cell: AND1
A B Y
Cell: INV2
A Z
EOF

my $fh;
my $cell;

my %lib1;
open $fh, '<', \$file1 or die "Can not open file: $!";
while (<$fh>) {
    chomp;
    if (/ ^ Cell: \s+ (.*) /x) { 
        $cell = $1;
    }
    else {
        my @ports = split;
        push @{ $lib1{$cell} }, \@ports;
    }
}

my %lib2;
open $fh, '<', \$file2 or die "Can not open file: $!";
while (<$fh>) {
    chomp;
    if (/ ^ Cell: \s+ (.*) /x) { 
        $cell = $1;
    }
    else {
        my @ports = split;
        push @{ $lib2{$cell} }, \@ports;
    }
}

my $diff = data_comparator(\%lib1, \%lib2);
print Dumper($diff) unless ($diff->is_empty());

__END__

$VAR1 = bless( {
                 'AND1' => bless( [
                                    bless( [
                                             bless( do{\(my $o = 'A')}
+, 'Data::Differences' ),
                                             bless( do{\(my $o = 'B')}
+, 'Data::Differences' )                                           ], 
+'Data::Differences' )
                                  ], 'Data::Differences' ),
                 'INV2' => bless( do{\(my $o = [
                                      [
                                        'A',
                                        'Z'
                                      ]
                                    ])}, 'Data::Differences' )
               }, 'Data::Differences' );
[download]

Thanks a BUNCH! This helps a lot! Just one more small help from you, i am not sure i fully understand what this portion does:

my $file1 = <<EOF;
Cell: AND1
A1 A2 Y
Cell: INV1
A Z
EOF

my $file2 = <<EOF;
Cell: AND1
A B Y
Cell: INV2
A Z
EOF
[download]

forgive me if its a stupid question! Thanks again!

The <<EOF syntax is known as a "here-doc", which you can read about in Quote and Quote like Operators.

I use it here to assign a multi-line string to a scalar variable. This was a convenient way for me to create a completely self-contained example which you could just copy-n-paste and run, without having to create 2 extra, external data files. Of course, in your application, you would read your 2 input files into your script.