Well here is one way of doing it -
int[] arr1 = new int[] { 1, 2, 3, 4, 5, 6 };
int[] arr2 = new int[] { 4, 6 };
List<int> list1 = new List<int>(arr1);
List<int> list2 = new List<int>(arr2);
IEnumerable<int> list3 = list1.Except<int>(list2);
int[] arr3 = list3.ToArray<int>();
Others might be having a better way of doing it.
Good luck.