Acharya Prashant clarifies that breathing is a habitual biological process rather than a natural one, explaining that the body functions as a conditioned machine. He emphasizes that freedom is not achieved by stopping physical processes like breathing or bodily demands, but by remaining unattached to them. He uses the analogy of wearing clothes to illustrate that one can inhabit a body without being a slave to its compulsions or identifying with its physical attributes like complexion or height. True freedom means the machine continues its functions while the individual does what they must do without being influenced by physical moods or identification.