There's no way to omit them from the call stack trace, as they are part of the call stack. If the stack trace gets logged they will appear.
If you're talking about how a tool like an IDE displays the call stack, I suppose an IDE with an advanced understanding of EE could know what class in your source code is your bean implementation and could offer a feature to collapse the call stack. That would be an IDE-specific feature. I have no idea if such a thing exists.