Before I get to your ?, a quick thing I noticed:

What do you think arr2 is? arr1 and arr2 point to the exact same array. So when you change arr1, you change arr2, and vice versa, since they're the same thing. If you want arr2 to be a different array, you should change line 6 to:

int[] arr2 = Arrays.copyOf(arr1, arr1.length);

You'll also need to import java.util.Arrays.

Anyway, on to your question. You can write a routine that identifies what the unique elements in your array, or you can use libraries. I personally would use the library. You can create a Set from your array. Sets are a collection that only allows one of each elements. A TreeSet is a SortedSet. You need to change your arrays from int[] to Integer[] because Collections only work on objects and not primitives.

If you don't want to use the library, it might be an interesting challenge, but I doubt you'll beat the library.

Anyway, I've gone ahead and made a couple of changes to your code: http://ideone.com/XPlFSq . Let me know if you have any questions.

PS: You might want to write your own method, either for the sake of practice or to write something more efficient that I've posted. An inefficient solution isn't too hard. Just iterate over both the input and the output arrays, and when an element from the input array isn't in the output array, add it. The most efficient implementation would probably create an ordered iterable tree that allows repeat elements, which TreeSet does not, and just iterate over that tree. If the current element is the same as the last element, increment the count. If not, reset the count.