If you want to do it with for-loops, then you will need so much loops as dimensions in the array.
i.e. (taking your code)
INPUT = new double [4][100]
IDEAL = new double []
for (int i = 0; i < 4; i++)
{
for int j = 0; i < 100; i++)
{
INPUT [i][j] = i+(j*2);
}
}
In conclusion if you cascade loops, you go through the different dimensions of your array.
If you start complicating it, you might think about having classes or using lists, maps or even a database.