1

Does this question sound natural:

What new features of C# have you used?

Or would you use another phrase, for example?

What new features of C# have you worked with?

3

To be honest, both sound perfectly fine. If I had to mark a difference between them, I would say that your second example sounds a bit more professional, like a question being proposed in an interview. Also, there is a mild difference in natural answers:

"What new features of C# have you used?"

In this case, you could honestly answer this question with any feature you have used once, although this may not be the intent of the question. Rather,

"What new features of C# have you worked with?"

This one seems to implicitly ask for features that you have used multiple times, features that you have a deeper understanding of and experience with. If you answer this with a feature you've only briefly used once, it may be construed as misleading.

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