We investigated the transmission of 7-keV Ne7+ ions through nanocapillaries of rectangular cross-section in phlogopite mica both by experiments and computer simulations. In the experiment, the role of the deposited charge in the transmitted ion intensity and angular distribution was studied. It is found that the rhombic angular profile is degraded during the process of rearrangement of the deposited charge on the capillary walls. Trajectory simulations are performed to understand the shaping of ion beam by the image force at tilt angles within the geometrical opening angle, as well as the degrading of the shaping due to the deposited charge when the tilt angle is larger than the geometrical opening angle. This reveals the interplay of the deposited charge and the image charge on the shaping of the ion beams when transmitting them through nanocapillaries of various geometrical cross sections.