In this study, optimization of the silicon nanopillar arrays and thin films coated on silicon substrate has been investigated in order to minimize the optical reflection loss from the silicon substrate surface. Nanopillars's filling ratio, pillar height, pillars diameter, sidewall incline angle, and step coverage with dielectric thin film thickness are systematically optimized together for the first time with these type of nanostructures. Full-field Finite Difference Time Domain method is used to simulate electro-magnetic fields and calculate the reflection from the modified nanostructured substrate surfaces in 400-1100 nm spectral range. Optimization recipe is clearly presented and this is not only useful for hexagonal arrays but also for regular arrays of nanopillars in general. We also further decrease the reflection by using step coverage concept which is the result of nonconformal coating on steps and trenches of thin films. We obtained approximately 2% of weighted average reflection in the 400-1100 nm range for perpendicular incident solar radiation which is one of the best results reported for this type of nanostructured surfaces in the literature.