Using 3-dimensional cell dynamics simulation, we demonstrate that the tetragonal phase of cylinder forming diblock copolymers can be induced on both topographical and chemical patterned substrates. The results quantitatively describe the different effect of both substrates on the degree of imperfection in the tetragonal phase observed in recent experiments [Xu, J.et al. Soft Matter 2011, 7, 3915]. Comparative analysis of the structural evolution for different thermal noise level in square, rectangular and diamond-shape lateral confinements is performed.