We can guide and encourage our minds, and develop mental discipline over time through daily practice.
Healthy self-control, though, is about embracing, accepting, and settling into peace, not about trying to get rid of negative thoughts. The effort to eliminate negative thoughts is violence against oneself, and always backfires. Take a look at what happened to OJ Simpson in the end - early on, a poster boy for the Power of Positive Thinking.
For more, see my hubs on Self Leadership and Self Management, on Self-Evaluation, and, on the more spiritual side, on Zen.