Prototyping is done, sometimes, to gain an understanding into the problem you're trying to solve. And sometimes, to get to know the underlying technologies if you are not already familiar with it.
For the case mentioned, you are considering to prototype in a scripting language, say, python and to make the actual code in C.
Evaluating some possibilities:
1. You prototype in python and write the software in C.
Prototyping in a scripting language can help where you quickly want to check output against input. This is useful if you primarily need to test the your logic for solving a problem. Also, useful if you want to quickly put together a demo for other people.
Whatever code you wrote in python will not be used in final software. But, it can aid if you are passing on your prototype to someone who can read python and write in C. Here, prototyping can help communicate an idea.
This method is appropriate for testing logical feasibility of the solution.
2. You prototype in C and write the software in C.
Prototyping in C, which is new to you, has two advantages. One, while you write the prototype, you get to understand the relevant parts of the language, library, API, pitfalls, etc. Two, while you build the final software, you can start from the prototype itself which saves you time and reuses code.
This method fits for testing both, the logical and technological feasibility of the solution.
3. You can consider non-coding ways to prototype depending on the problem at hand.
If it some piece of logic and ideas you want to prototype; pseudo code, flowcharts and block diagrams on paper is good too.
If it is a UI prototype, consider some UI mock-up tool or again, some paper.