deryaaltuntas,
I am afraid MyEclipse does not provide an intrinsic support for 3D programming. If you have an eclipse based plugin which does that, you can add the same to your ME profile and give it a shot. You mention you have installed Java 3D API. Can you elaborate more on this. How did you add Java 3D API to your ME profile? You also mention that you are missing a lib file. In case this library is not available, you can add the same to your project as a user lib.