Currently it is not possible to remove individual map features. You can hide all the settlements (Details > Towns > Hidden). Or you can remove a specific settlement from the almanac ([Town name] > Remove from almanac), but this only removes its name from the legend.
It is very easy to remove a town icon from an exported SVG. For example, you can open it in Chrome, right-click the icon and choose "Inspect". Then right-click the enclosing group of the highlighted element (that will be the group for the whole icon) and choose "Delete element".