Geetha:
You can expect to spend at least $5000 for a set of 100 custom "professional" polycarbonate molds. The main cost is going to be making the injection mold master. This is tooled in metal and is made so that the molten polycarbonate plastic can be forced into the mold. As you might imagine, a mirror-smooth finish is required on the mold surfaces in order to deliver the perfectly shiny results on your bars.
You are right - they are much more durable than the thin thermoform molds you are familiar with. Which is best for your depends on many factors.
One option to consider is that there are tabletop thermoforming machines that cost well under $1000 that can handle plastic sheets at least as large as for a standard mold. The tooling costs for making a master for use in one of these machines is much, much lower than for an injection mold and you can make new molds for a few dollars apiece. Thermoform plastic sheets come in a variety of thicknesses, so you can choose between different thicknesses for different reasons - thinner plastic might resolve finer detail better, thicker plastic is more durable.
I looked into this for one project, and it cost about the same to buy the thermoform machine as it did to have someone do the work. They would make the master from a computer CAD (CNC) file we sent them, but if you have a local machine shop they might be able to help. (Or go to a technical training institute where the teach such stuff and see if you can get a teacher to get a student to do it for you ... not for free, of course.)
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clay - http://www.thechocolatelife.com/clay/