I think your problem seems not being caused by the code you show us. It is probably caused in the construction the arrays. You might have used the method below: 
$array2[$n] = $array1[$n];

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Because your two arrays are complex, this does not copy the structure and content, but only copy the corresponding reference. So the value $n in @array2 actually points to the value $n in @array1.
In addition, while asking questions, please make your code more refined, for example: 
for my $i (0..$#array1) {
    for my $j (0..$#array2) {
        # do something
    }
}

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In reply to Re: Updating 1 array affects the other array by llancet
in thread Updating 1 array affects the other array by iphony

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