1/4 inch in size eh? Hmmm.... Thermoformed mold probably won't work for you. Essentially what thermoformed mold is a sheet of heavy plastic laid over top of a "negative" of the mold, heated almost to melting point, and then sucked down on to the negative by vacuum pressure. The detail is nowhere near the clarity of polycarbonate, and is certainly not going to get you the 1/4 inch inclusion squares you want.
Polycarbonate molds are essentially little pellets of plastic that are melted and then forced into a metalmold shape under intense pressure and heat. The plastic cools and then the mold is popped open to let out the molded shape - which is usually very hard and clear (some are white). A machine that could handle a 2 foot sized mold would be huge. I'm sure they are out there, but holy cow your molds will be expensive. Prepare to sell off your first born for those bad boys!
My suggestion would be to create a negative out of wood, or molding clay, or something like that, and then use silicone. You can then make your own. There are lots of videos online to do that, and most cities have craft stores where silicone molding supplies are sold.
Hope that helps.