Homo-epitaxial (100) single crystal diamond films of different isotopic (13C) composition were synthesized by micro-wave plasma chemical vapor deposition (MPCVD). Undoped 12C (100) films were also synthesized at different thicknesses. The growth surface of 13C doped showed a sequential morphological change from flat surface to stepped or ledge surface and coarsening of the steps/ledges with the increase of 13C-isotope concentration. As the growth proceeds via surface steps/ledges and coarsening of these steps/ledges, further increase in imperfection of the grown CVD single crystal diamonds observed with the development of non-(100) orientations. In case of undoped 12C samples, as the thickness increased the in-grain misorientation got reduced.