Hi Sancheuz and David,
@Sancheuz, I tried using conform and shape merge tool both in 3dsmax, but the terrain mesh is just too crude and huge to work on that. Every time I tried to use those two above tool, it didnt work. I also had to refine the mesh by removing broken vertices, double edges etc but still it didnt work.
@David, I tried using booleran, but 3dsmax crashed couple of time before I stopped using that. Its because the mesh is around more than 1 million polys. The Anti-stitcher looks nice, I will see if I can use this effectively on the terrain.I even tried with Glue plugin, but it failed as well.