Have you imagined that meditation is stopping all thoughts? That is like trying to stop the wind. Let the wind be while you take shelter in the stillness of the Self. Thoughts may continue but they need not disturb you or interrupt your meditation. The wind doesn't blow all day. Eventually it quiets down. Give no regard to thought activity and it will subside.
~Ellen Grace O'Brian from her book Living for the Sake of the Soul
When we first begin our meditation practice most of us think that our thoughts should be completely eliminated. We get frustrated when they aren't and that frustration may stop our practice. What we don't realize is that our thoughts are a part of us and don't completely go away, but they subside with our regular meditation practice. We learn not to notice them and allow them to pass by. It is like clouds in the sky. The clouds are the thoughts but we are focusing on the clear stillness of the sky. The thought activity will subside. Be patient.