Guiding of the phase separation of a block copolymer (BCP) by an electric field perpendicular to the substrate is investigated in order to obtain vertical structures that can provide a mask for subsequent etching. Because of practical aspects, the substrate is bare Si without any neutral brush and the process time is limited to 1 h. A polystyrene-block polymethylmethacrylate lamellar material is employed in the study. For a unique guiding of the lamellar phase, an ordering mechanism orthogonal to the electric field is introduced by the interaction with the stamp in a thermal nanoimprint process. The naturally low surface energy of the stamp shall induce the formation of lamellae along the sidewalls of linear cavities. In order to fully utilize these two ordering mechanisms, the stamp sidewalls and the electric field, the imprint process is conducted in such a way that no residual layer remains below the stamp structures and the whole BCP is accumulated inside the cavities which are just partly filled. The electrically-assisted imprint process is studied analytically, considering the capacitive effects due to the local electric field in the cavity and in particular in the BCP. In addition, a numerical simulation is performed for the actual experimental conditions to compute the electric vector field in the BCP. In this way, an extensive understanding of the situation is gained which is the basis for choosing optimal experimental conditions for electrically-assisted thermal nanoimprint. Furthermore, the ambiguity of the electric field in a thermal nanoimprint process with partly filled cavities is addressed. The field shall induce vertical phase separation but, due to instabilities, it also may induce capillary bridges that represent replication defects. An improvement of the vertical phase separation by applying an electric field as high as 25 V/μm could be identified under specific experimental conditions. However, the guiding effect within the cavities and thus the long-range order of the lamellae remained limited. This may be due to a field strength too low in the BCP; in the present configuration, higher field strengths are prohibited by an electrical breakthrough.