Orientation of anisometric layered silicate particles subject to shear flows has always been a crucial factor in the final microstructure of polymer nanocomposites in polymer processing. Plenty of experimental works and theoretical investigations have been conducted in order to provide an accurate understanding of the phenomena involved. The development of coarse-grained molecular simulation methods in recent years has made it possible to explore more details of pre-described systems under a variety of conditions. Dissipative particle dynamics (DPD) being one of them, has been widely applied to study multicomponent materials. With the introduction of Lees-Edwards boundary conditions, DPD was soon found to be an efficient method to simulate hydrodynamic systems considering its ability to access longer time scales compared with classic molecular dynamics. Here, we report on the orientation of a semi-flexible 3-layered silicate particle embedded in a polymer matrix while imposed to shear flows. By applying different shearing directions, the evolution of the orientation process from rest was recorded. 2D pair distribution functions in 3 orthogonal planes were calculated in order to provide a full description of the systems. For all directions regardless of the initial orientation of the layered silicate, it was found that the layers rearrange so that their surface would be normal to the velocity gradient direction. At low shear-rates, the orientation process was found to be unstable and ascribed to the thermal fluctuations and the instabilities in the velocity gradient throughout the system. Such a behavior was almost eliminated when the shear-rate and subsequently the Peclet number were increased. The calculation of the angles between the silicate layers and the flow and velocity gradient directions proved that no matter how the layers are oriented initially, the evolution pattern of an oriented microstructure becomes smoother and faster with increasing the shear-rate.