Is it possible to destroy an object at a specific position?

Is it possible to do something like this?

GameObject.Destroy(Object(0,0,0));

No, that is not possible. You have to know which GameObject is at that position. If you are making a grid-type game, you can make a jagged array which contains a GameObject at each specific index = position.

So if your grid is, say 5 by 4 you will have a jagged array like this:

GameObject[][] objectsInMap = new GameObject[5][]

Then, use a for-loop to initialize each index to 4:

for (int i = 0; i < objectsInMap.Length; i++)
{
    objectsInMap *= new GameObject[4];*

}
Then, when you need to destroy a GameObject at a specific position, use:
if (objectsInMap[x][y] != null)
{
Destroy(objectsInMap[x][y]);
}

You could create a collider at the desired position, set it to trigger and attach a script with an OnTriggerEnter event method that could handle the object destruction.