Does this work for you?

use strict;
use Data::Dumper;

my @data;

while (<DATA>) {
    chomp;
    push @data, [ split '\s', $_ ];
}
@data =  sort { $a->[1] <=> $b->[1] or
                $a->[2] <=> $b->[2] } @data;
print Dumper \@data;
__DATA__
A 00006360 A001002002 000000000.00
A 00006360 A001012012 000000000.00
A 00006360 A001054054 000000000.00
A 00005460 A001102002 000000000.00
A 00007360 A003015015 000000000.00
[download]

I'm not sure what you meant by having 'A' in the third column disregarded. If you meant you didn't want it in the data, change the while loop to the following:

while (<DATA>) {
    chomp;
    push @data, [ split '\s', $_ ];
    $data[ -1 ][ 2 ] = substr( $data[ -1 ][ 2 ], 1 );
}
[download]

If you want it included but disregarded in the sort, change the sort to the following:

@data =  sort {         $a->[1]     <=>         $b->[1] or
                substr( $a->[2], 1) <=> substr( $b->[2], 1) } @data;
[download]

Cheers,
Ovid

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