Pre-Tuned cars can be tuned but cannot be modified/customized. To tune a Pre-Tuned car, take it to a race day with a race that the Pre-Tuned car can enter. Then select race events in the race day menu, select a race your Pre-Tuned car can participate, choose practice, and use your Pre-Tuned car. When you entered practice and the practice has begun, press start.
You should see a CAR TUNING menu. Select that menu. Voila, you can now tune your Pre-Tuned cars!