Block copolymer thin films with tunable surface chemistry and nanoscale self-assembled structures are promising candidates as advanced templates for inorganic crystallization. Their periodic order, nanoscale spacing and precise control of surface chemistry in one block allow them to confine the crystal nucleation and growth both physically and chemically. In this work, a poly(styrene-b-(3,4-isoprene-stat-1,2-isoprene) (PS-b-(3,4-PI-stat-1,2-PI)) thin film system was developed, optimized and characterized by atomic force microscopy (AFM). Stable PS-b-(3,4-PI-stat-1,2-PI) thin films in an aqueous environment were achieved via substrate modification of silicon wafers. Furthermore, thin film blends with different amounts of hPS mixed with PS-b-(3,4-PI-stat-1,2-PI) BCP were prepared and investigated in order to achieve periodic well-like surface structures, similar to what had been achieved for PS-b-P(AGE-co-EO) thin films. Finally, post-fabrication functionalization of PS-b-(3,4-PI-stat-1,2-PI)/hPS was performed with amino acids, demonstrating that thin film surface structure before and after functionalization was maintained both in air and in aqueous solutions. This approach demonstrated a new materials platform providing reliable structure and chemistry stability for aqueous crystal templating processes.