Autodesk's
123D suite of free tools could help you with that project. By using
123D Design, you could trace the outline and extrude it up. More importantly, 123D Design has Fillet/round tools that will round the edges nicely, with whatever radius you specify. If you are making a bubble pack for a large item, you could either print that model, or build a more durable tool by using
123D Make to slice the model into layers that could be cut in 1/4" plywood by laser, scroll saw, or even a jigsaw and dremel. From there you would sand or fill to smooth the stepping.
One important note is that most 3D-printing materials are thermoplastic and would probably not survive vacuum forming. The best material in that case would be Sandstone (Plaster coated with super-glue), which you would want to be between 5-10mm thick, possibly with internal support walls/struts.
I'd also like to let you know that I have had the most success with the PC versions of the 123D software. The browser, Ipad, and Mac versions still had a few bugs the last time I checked.
Edit: re-reading your description, I see you are actually trying to build a jig (template) for your router. I still recommend the above process, as it would save the labor of manually routing each copy, and allow you to have arbitrary radius' and other complex shapes in your design.