I suspect that you really want to store the coordinates as a four-element array as opposed to a 4-dimension array. The following might serve as an executable example of what you want:

use strict;
use Data::Dumper;

my %zones;
while (<DATA>) {
    chomp;
    my ($zone, $a1, $a2, $b1, $b2) = 
        $_ =~ /(\w+) = (\d+),(\d+),(\d+),(\d+)/;
    #append an anonymous (coordinate) array on to the
    #anonymouse array that is the value for each hash
    #key in %zones hash.
    push @{$zones{$zone}}, [$a1, $a2, $b1, $b2];
}
print Dumper(%zones);

__DATA__
B1 = 11,21,3,59
B2 = 1,23,7,51
B1 = 9,2,11,9
B2 = 1,23,7,59
B3 = 3,92,12,13
B1 = 2,2,18,50
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