There are several steps you can take to secure your PCB design from being reverse-engineered and copied. Every added security step will make it more difficult to copy your design, at some cost to you; there is no way to ensure the design is completely copy-proof. Furthermore, you will have to reveal some internal/secret details of your design to somebody, at some point -- somebody needs to actually manufacture it, after all. Somebody needs to write code for it.
A determined organization with an unlimited budget will always succeed in reverse-engineering your product. Your goal is really to make the reverse-engineering process unprofitable.
As such, here are some suggestions, generally listed in order of less-expensive to more-expensive.
- Packaging. Make it difficult for anyone to open the device; hidden latches, secret screws, short wiring harnesses, adhesives.
- Apply opaque conformal coating or potting to the PCB, to obscure the parts you've chosen.
- Etch or scrape the part numbers off of chips. They might know you're using an SOT-23, but which one?
- Design a 4+ layer board. Use blind or buried vias and internal signal lines.
- Design two separate boards connected by a header, card edge, or ribbon cable. Have each half made by two different manufacturers.
- Design a copy-protection subcircuit, e.g. some small microcontroller running an encryption algorithm to verify the board's authenticity to an external device.
- Assemble your board in-house. Keep your parts list a secret to everybody outside of your organization.
- Manufacture the PCB, or the entire device, in-house.
In my understanding, most intellectual piracy is the result of some trusted person spilling a secret. The fewer people who know your secrets, and the harder you make it for an outsider to figure them out, the less likely that you will be a victim of piracy.
Finally, a couple words of warning:
The most successful designs in history have been the most hackable. Are you sure you want to go through all this effort to protect your work, if it means nobody's going to use it anyway? Most likely the early adopters will just pick a different device/tool/ecosystem entirely.
Nothing's stopping anybody from stealing your idea. Is your design so revolutionary, and so creative, that anybody who sees your device can't just sit down and design their own? Is your work even patentable? Is it really worth the effort to obscure design details that aren't even necessary for the functionality of the final product?