How can i stored x and y coordinate in two dimensional array in c#

Dude.. my understanding is that you have got 40 points having x and y to be stored.

1) You can use an array like you mentioned:
int[,] array = new int[40,2];
array[0, 0]=100; //x
array[0, 1] = 200; //y

or

2) Use the Point struct and List for storing
IList list = new List();
list.Add(new System.Drawing.Point(100, 200));