When you initiate the array (i.e. int[][] array = new int[20][20];) every position is already filled with 0 (since a primitive cannot be null). So, if zero is not one of the numbers you are using, simply cycle through the arrays with a nested loop replacing 0 with 99.

Agree that a premitive cannot be null. But what if one of the position is actually filled with number zero [0] from a text file (zero also being a number) and should not be replaced with 99?

Are you using Java 1.5 or later? If so, make it an Integer array, rather than an int array. Then "empty" spots will be null and you just (after having filled it with the random numbers) cycle through with an == null check. And, you can still do array[i][j] = 1; or some other int, because autoboxing will automatically convert it to an Integer. You can also, later, use the Integer as if it were a normal int. That seems to be easiest solution.