Control over the alignment of colloidal structures plays a crucial role in advanced reconfigurable materials. In this work, we study the alignment of Janus particle lamellar structures under shear flow via Brownian dynamics simulations. Lamellar alignment (orientation relative to flow direction) is measured as a function of the Peclet number (Pe)-the ratio of the viscous shear to the Brownian forces-the particle volume fraction, and the strength of the anisotropic interaction potential made dimensionless with thermal energy. Under conditions where lamellar structures are formed, three orientation regimes are observed: (1) random orientation for very small Pe, (2) parallel orientation-lamellae with their normals parallel to the direction of the velocity gradient-for intermediate values of Pe, and (3) perpendicular orientation-lamellae with their normals parallel to the vorticity direction-for large Pe. To understand the alignment mechanism, we carry out a scaling analysis of competing torques between a pair of particles in the lamellar structure. Our results suggest that the change of parallel to perpendicular orientation is independent of the particle volume fraction and is caused by the hydrodynamic and Brownian torques on the particles overcoming the torques resulting from the interparticle interactions. This initial study of shear-induced alignment on lamellar structures formed by Janus colloidal particles also opens the door for future applications where a reversible actuator for structure orientation is required.