The influence of Mn flux intensity and growth temperature on surface morphologies of III-V based magnetic semiconductor (Ga,Mn)As layers grown by low temperature (LT) molecular beam epitaxy (MBE) on (001) GaAs is studied by atomic force microscopy (AFM). The results show that homogeneous (Ga,Mn)As grows two-dimensionally (2D), whereas 3D growth takes place when hexagonal second phase appears on the growth front.