My idea would be to make a model out of something that is naturally hard or sets hard, so carving or building using wood, plastic, modelling clay, metal, fondant etc. and super glue it to the top of a spare keycap, then made a mold of this.
Of course another way to do it would be to make a mold of 2 caps stuck together, and carve the top cap into the shape you want.
First way would be good to mass produce the same design, but you use a cap for every new model.
Second way would be great for 1 offs, and you would only ever need use the original 2 caps for additional molds, but if you really like a piece you would have to make a mold of your 1 off piece and risk destroying it in the process.
Either way has benifits and flaws, but personally I would do it the first way.