You're probably not using the right tools, but given the circumstance and information I would either use Array::Unique or load them into a hash as keys and then read the keys of the hash.

my %_;
map { %_{$_} = undef } @arr1, @arr2;
my @newarr = keys %_;
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Miss-read question, working this out again sry,
What your going to want to do is splice the array, to delete the elements, but that solve the problem of duplicate elements in one array, ie.

  @a = (1,2,3,4,5);
  @b = (1,3,1,3,1);
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You want the second list to be empty? and the first list to have (2,4,5)?