Rapid evaporation of solvent from spray colloidal droplets induces directed self-assembly among the nanoparticles, eventually interlocking them into correlated granular structures. In this work, it is demonstrated that anisotropy in colloidal interparticle interaction plays a key role in governing the surface topology of spray-dried granules. Colloidal dispersion comprised of spherical nanosilica (NS) and cylindrical carbon nanotubes (CNT) was chosen as a model system in this regard. For identical polarities of the colloidal components, granules with prominent wrinkle-like modulations are obtained, which is in drastic contrast with the case of opposite polarities. The extent of surface modulation depends on the relative concentration of CNT with respective to NS. A plausible mechanism for the formation of surface modulation is elucidated on the basis of the evolving anisotropic interparticle interactions during assembly. Electron microscopy, small-angle scattering, Raman spectroscopic techniques have been used for quantitative characterization of these micro-granules.