We demonstrate that the shear alignment and the shear-induced transitions in sphere-forming diblock copolymer single layer and bilayer films observed experimentally [Y.-R Hong, D. H. Adamson, P. M. R. A. Register, Soft Matter, 2009, 5, 1687] can be explained by cell dynamics simulation, a simple model with a Ginzburg-Landau Hamiltonian. In two layer films the spheres align in various arrangements, like (100) or (110) bcc planes, or transform to cylinders depending on the shear rate and the temperature. For the first time, we present a nontrivial alignment mechanism of a single layer of spherical domains in shear via slug-like movement of transient cylindrical micelles. In addition, we clarify the formation of the perpendicular cylinders, found in the recent particle based simulation [A. Chremos, K. Margaritis, A. Z. Panagiotopoulos, Soft Matter, 2010, 6, 3588].