Block co-polymer patterns are attractive candidates for nanoparticle assemblies. Directed self-assembly of block co-polymers in particular allows for long range ordering of the patterns, making them interesting scaffolds for the organization of magnetic particles. Here, a method to tune the channel width of polymer-derived trenches via atomic layer deposition (ALD) of alumina is reported. The alumnia coating provides a much more thermally robust pattern that is stable up to 250 degrees C. Using these patterns, magnetic coupling in both ferromagnetic and superparamagnetic nanocrystal chains is achieved.