As discussed in similar questions here and here I want to protect my code from reverse engineering.
My situation is as Simucal describes in his (excellent) answer h
You should obfuscate the complete code since it gets harder to reach that small valuable part. The smaller the code gets, the easier it becomes to understand it. Most obfuscators should not mess with public interfaces since there are many obfuscated libraries out there.
However I think you should rather convince users that there are no special tricks there instead of trying to hide it. To quote Kaiser Soze, "the greatest trick The Devil has ever pulled is to convince the world that he doesn't exist".
And of course you can always file a patent for your invention and protect yourself legally.