Being an engineer, this topic is very interesting to me. Thought I would throw in my 2c.
If it were me, I would model the bait rather than the mold. I'd want to see my finished product, not the cavities.
Any of these CNC mold makers on TU should be able to subtract your model from a mold base to make the cavities.
But like some have said, the model has to be "moldable" and "millable" (No undercuts, and no excessively small radii).
The only "affordable" 3D CAD software I have seen out there is Alibre at ~$300.
I would download the Trial Version to see how user friendly it is.
I agree!!!
Once I upgrade my home PC, I plan on putting software on it for that exact purpose.