The notions of the self that Buddhism refutes may be commonsensical and intuitive, but they're not those of the philosophical and scientific reconstruction. Most religions think of the self as an eternal, immaterial spirit, as indeed a unified perceiver of all our mental states that's conscious and therefore separate from the body. Buddhism denies there's such a self, which is fine.

But that's irrelevant to naturalistic philosophy which likewise denies there's a self in that traditional sense. What there are are the mind and the brain and the body. The brain's function is to produce the mind. The mind is a series of thoughts and feelings that fall into certain patterns and habits, based on the person's genes, upbringing, culture, experience, and memories which form her character/personality/mental individuality.

There are personality tests, for example, that distinguish between different kinds of people, based on the types of thoughts and goals they tend to have. That pattern helps distinguish one self from another. That's mental rather than physical individuation.