The orientation of hexagonal boron nitride (BN) nanosheets was controlled in polymer-based nanocomposite film using microscopic molds while applying a dc electric field. The hexagonal BN nanosheets were dispersed by sonication in a prepolymer mixture of polysiloxane followed by high speed mixing. The homogeneous suspension was cast on a microscopic mold with different patterns, which was attached to a positive electrode during application of an electric field before it became cross-linked. Analysis revealed that filament-like linear assemblies of BN nanosheets (LABNs) were fabricated in polysiloxane/BN nanosheet composite films, and the LABNs were aligned perpendicular to the film plane with high anisotropy. The anisotropy of BN nanosheets and dimensions of LABNs were directly related with the thermal properties of the composite, and could be changed according to the type of microscopic mold used. LABN formation and the heat conduction mechanisms induced by the type of microscopic mold and the intensity of the applied electric fields are discussed.