When I used the brush size of 3 X 3 (i.e. too small brush size), the deformed terrain position is not exactly at position(3d point) given to deform the terrain. How can I overcome that problem.
You can't. Deforming takes place on a fixed grid (namely, the terrain heightmap), so the brush needs to be aligned on that grid. Any position in-between is not working. The best way to to deal with this problem right now is to have your brush be aligned on that same fixed grid. You can read a bit in these forums, there are recipes to do that.
ETL v3 uses interpolation to allow deforming at non-grid positions. But with such a small brush it may still not be enough to hide the problem. If you need such detailled editing, you will have to increase the number of terrain vertices your terrain uses.