Large area microdomain alignment in poly(ethylene oxide-b-6-(4'-cyanobipheny1-4-yloxy) hexyl methacrylate) block copolymers was successfully accomplished by the application of a 6 T magnetic field while cooling from elevated temperatures in the melt state. Small-angle X-ray scattering demonstrated that lamellar and cylindrical PEG microdomains aligned with their interfaces along the applied field, whereas the smectic layers of the liquid crystalline mesophase are perpendicular to the field. This is in agreement with the positive diamagnetic anisotropy of the cyano-biphenyl mesogen and a homogeneous anchoring condition at the intermaterial dividing surface (IMDS) between the two blocks. The alignment of the system is driven by the diamagnetic anisotropy of the smectic mesophase and not by the crystallization of PEG at lower temperatures. The addition of poly(acrylic acid) and LiClO4 salt result in the suppression of PEG crystallinity and stronger segregation between the polymer blocks leading to improved order in the material. The resulting films are well aligned over millimeter length scales of area and thickness. We use a novel continuous rotational annealing approach to break the degeneracy of the lamellar alignment, permitting facile directed assembly of the system during a single cooling step. Our experiments demonstrate the creation of well-aligned arrays of amorphous PEG domains over large length scales and offer a route to functional materials, in particular, for selective transport applications such as solid ionic electrolytes.