Films of self assembled diblock copolymers (BCPs) have attracted significant attention for generating semiconductor nanoarrays of sizes below 100 nm through a simple low cost approach for device fabrication. A challenging abstract is controlling microdomain orientation and ordering dictated by complex interplay of surface energies, polymer-solvent interactions and domain spacing. In context, microphase separated poly (styrene-b-ethylene oxide) (PS-b-PEO) thin films is illustrated to fabricate nanopatterns on silicon and germanium materials trenches. The trenched templates was produced by simple electron beam lithography using hydrogen silsesquioxane (HSQ) resist. The orientation of PEO, minority cylinder forming block, was controlled by controlling trench width and varying solvent annealing parameters viz. temperature, time etc. A noticeable difference in microdomain orientation was observed for Si and Ge trenches processed under same conditions. The Ge trenches promoted horizontal orientations compared to Si due to difference in surface properties without any prior surface treatments. This methodology allows to create Ge nanopatterns for device fabrication since native oxides on Ge often induce patterning challenges. Subsequently, a selective metal inclusion method was used to form hardmask nanoarrays to pattern transfer into those substrates through dry etching. The hardmask allows to create good fidelity, low line edge roughness (LER) materials nanopatterns.