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In this paper, the effects of residual charges on nanofiber alignment in a gap method are studied and presented. The gap method was presented by Li and Xia (2003 Nano Lett. 3 1167); in it, a gap is introduced into a traditional collector. Due to the non-perfect conductivity of electrospun nanofibers, they carry residual charges after deposition across the gap. These residual charges will interact with the charges carried by the upcoming jet/fiber, that will also deposit across the gap. The effects of these charge interactions on nanofiber alignment were studied numerically at various gap sizes. Results showed that alignments of nanofibers improve substantially with the gap size increasing from 3 to 8 mm. Numerical studies on the effect of residual charges in already deposited nanofibers on the alignment of nanofibers deposited afterwards were also conducted. Studies showed that the residual charges result in worse alignment, with a 10%–25% decrease in orientation parameters.