I will use a for loop inside a for loop to compare element 1 of array 1 with all elements of array 2

Nested for loops over two arrays might not be the best option. Consider loading the data of array 2 into a hash and using a look-up into the hash. This should be much faster and also easier to code.

You don't give enough details for me to be able to be more specific, but "array 3" might also be better designed as a hash.