How can I file a complaint against the police department for bullying my car?

Just follow the law . You can place a formal complaint with the dept but this may just cause you more issues. What you should do is get the officers info when they pull you over Badge number etc if one officer is the one who is doing this you may be a target and can place a formal complaint with his department . But if its many officers there may be something more to your story than your stating.