Per se is the phrase to use when you want to refer to a particular thing on its own. It is not this Latin phrase, per se, that is important, but rather the concept it represents.
Per se is handy when you need to single out a particular element of a bigger thing. So you might say, "The song, per se, wasn't a bad choice; it was your singing voice that was atrocious." In Latin it means "by itself." When you want to sound a little smart, inject a per se into what you're saying. It's one of those phrases, like "insomuch" or "as it were," that helps win arguments.