A combination of electromagnetic alignment and topological pattern assisted alignment to position magnetic nanowires, which is referred to as the Patterned Electromagnetic Alignment (PEA), is developed and examined. Electrodeposited, FeNiCo nanowires with different lengths were used as the test nanomaterial, and the microscale grooved surface was formed by UV nanoimprint lithography. The accuracy of the PEA with FeNiCo nanowires was evaluated by measuring the deviation angle from the direction of the magnetic field line for different magnetic field strengths and nanowire lengths, and a statistical alignment distribution was reported for different nanowire length groups. The results were compared with those of the electromagnetic alignment on flat surfaces and in grooved-patterned substrates without electromagnetic alignment. Overall, the deviation angle for the PEA was lower than that for the electromagnetic alignment when all other experimental conditions were identical, indicating that the alignment accuracy along the direction of the magnetic field lines was enhanced in the presence of surface micro grooves. This can be attributed to the fact that, upon attachment of nanowires to the substrate surface, the surface micro grooves in the PEA add additional deterministic characteristics to the otherwise stochastic nature of the nanowire deposition and solvent evaporation processes compared to the sole electromagnetic alignment.