This paper is the second in a two-part exposition on surface-directed spinodal decomposition (SDSD), i.e., the interplay of kinetics of wetting and phase separation at a surface which is wetted by one of the components of a binary mixture. In our first paper [P. Das, P. K. Jaiswal, and S. Puri, Phys. Rev. E 102, 012803 (2020)2470-004510.1103/PhysRevE.102.012803], we studied SDSD on chemically heterogeneous and physically flat substrates. In this paper, we study SDSD on a chemically homogeneous but morphologically patterned substrate. Such substrates arise in a vast variety of technological applications. Our goal is to provide a theoretical understanding of SDSD in this context. We present detailed numerical results for domain growth both inside and above the grooves in the substrate. The morphological evolution can be understood in terms of the interference of SDSD waves originating from the different surfaces comprising the substrate. © 2020 American Physical Society.