I'm actually using Adobe Illustrator, but you could get the same results using any vector program. Inkscape could do this easy as pie, I'm just more accustomed to Illustrator. All you really want is a vector program that has good layer management.

The only thing I'm doing so far is manually adding basic white shapes with the pen tool with a white fill. The walls are the same path, copied so you have one on top of the other, then I colour the top path a light colour and make the bottom, black path wider. Only thing that makes such a process annoying is a) the time it takes (but I listen to documentaries while I draw, so that's ok) and b) the hand cramps from holding a pen for so long.

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Also, I've made separate layers for everything. Obviously the terrain is one layer, with sub-layers for each elevation and the river. Another layer for all the defensive fortifications with separate groups for every set of walls, towers and gates. Then every city quarter has it's own layer. Finally, within every city quarter layer I'm grouping the "gardens" separately from the built up areas. Then there is a separate layer for the "named" buildings, which are going to be tagged in the final legend, so I'll find them more easily.

After the drawing itself will be done, there will be some more layers for grids, wiggly bobs and other thingamajigs too ...