We study the shear-induced alignment transition from transverse to the shear plane to parallel and perpendicular in a lamellar or smectics system. A recently proposed simple continuum model for amphiphiles is studied by large-scale nonequilibrium molecular dynamics simulation. We find a shear-rate dependence of the alignment transition under shear flow, parallel at low and perpendicular alignment at high shear rates. To identify the alignment and degree of order of these shear-induced orientations by scattering, a 3D analysis of the scattering data is needed.