Clonazepam works by enhancing the effects of a naturally occuring body chemical called GABA (gamma amino butryic acid). In the brain and central nervous system GABA will attach to a cell's benzodiazepine receptor. When this happens it inhibits or even ceases the nueron from firing, effectively "calming" or "slowing down" brain activity.
Clonazepam works by enhancing the ability of GABA to attach to the benzodiazepine receptor. It makes the attachment easier and more effective, allowing the body's supply of GABA to work much more effectively.
Basically, think of the benzodiazepine receptor as a pair of shoes that is one size too small, GABA as your foot, and clonazepam as a pair of extra thick wool socks. The extra thick wool sock allows for a much better fit with shoe, and that better fit makes walking, running, etc. much more effective. A crude analogy but the best one I can think of at the moment.