We investigated transmission characteristics of Ne7+ ions through nanocapillaries of rectangular cross-section. The capillaries were produced by chemical etching of ion tracks in phlogopite mica. The two dimensional transmission profiles are rhombic when the capillaries are tilted at angles smaller than the geometrical opening angle given by the aspect ratio of the capillaries. For the angles larger than the geometrical opening angle with respect to the beam direction, the rhombic profile is degrading. Possible reasons for the degrading of the shapes by the deposited charge inside the capillaries are investigated and discussed.