The ionospheric signature of a flux transfer event (FTE) seen in EISCAT radar data has been used as the basis for a modelling study using a new numerical model of the high-latitude ionosphere developed at the University of Sheffield, UK. The evolution of structure in the high-latitude ionosphere is investigated and examined with respect to the current views of polar patch formation and development. A localized velocity enhancement, of the type associated with FTEs, is added to the plasma as it passes through the cusp. This is found to produce a region of greatly enhanced ion temperature. The new model can provide greater detail during this event as it includes anisotropic temperature calculations for the O⁺ ions. This illustrates the uneven partitioning of the energy during an event of this type. O⁺ ion temperatures are found to become increasingly anisotropic, with the perpendicular temperature being substantially larger than the parallel component during the velocity enhancement. The enhanced temperatures lead to an increase in the recombination rate, which results in an alteration of the ion concentrations. A region of decreased O⁺ and increased molecular ion concentration develops in the cusp. The electron temperature is less enhanced than the ions. As the new model has an upper boundary of 10 000 km the topside can also be studied in great detail. Large upward fluxes are seen to transport plasma to higher altitudes, contributing to the alteration of the ion densities. Plasma is stored in the topside ionosphere and released several hours after the FTE has finished as the flux tube convects across the polar cap. This mechanism illustrates how concentration patches can be created on the dayside and be maintained into the nightside polar cap.<br><br><b>Key words. </b>Ionosphere (ionosphere-magnetosphere interactions; polar ionosphere). Magnetospheric physics (magnetopause · cusp and boundary layers)