Many times, software companies feel like they have a binary choice: protect their software with trade-secret policies or register the software at the Copyright Office.
Either instinctively or based on advice, they know that you can't protect a trade secret if it isn't secret anymore. And registering software at the Copyright Office requires sharing a deposit with the government. So they assume that if they register the software, they can't protect the value of the trade secret. But this is not true.
First of all, you are not required to deposit all of your source code to register your program—just the first 25 and last 25 pages. It could be that what is really valuable—as a secret—in your code isn't in those pages. So registering your code and maintaining your trade secrets are not mutually exclusive.
Second, even if your trade secret is included in those parts of the code, the Copyright Office allows for other types
of deposits, if trade-secret issues require it. An attorney can help you navigate the deposit regulations to maximize your copyright and trade-secret protection.