Zen meditation is often misunderstood as a practice of stopping thoughts or having no thoughts but it's actually a practice of noticing thoughts. Zen is not about eliminating thoughts but illuminating them.
There's no need to repress thoughts or ignore them. There's no need to judge them or scold them. Simply notice the thoughts. Be aware of them. And if you find yourself repressing, ignoring, judging, or scolding your thoughts, there's no need to repress, ignore, judge, or scold that.
— Kim Boykin, Zen for Christians