My magic system is based on the mind fundamentally altering the properties of matter for short periods of time. But it should be limited to non-living subjects. The magic has to do with the physics of the object, not the biology. Also, having magic is rare.
Also, it would be nice if whatever method could still work on wood, though not necessarily on living trees.
Your subconscious mind overwrites any attempts to alter your body, both your own and other peoples. If magic is a manifestation of your mind, then the subconscious mind is also able to manipulate magic. The subconscious mind has much stronger reactions than our conscious mind, so the equilibrium of your body is maintained by the subconscious mind, like an extra biological process. That way no matter how strong a conscious thought is, it cannot overcome the subconscious mind.
With this system in place, you can write the rarity of magic as "most people can't draw any magic away from the subconscious, only those with strong thought patterns can draw off the mana used by the subconscious mind. The more they want to use, the harder they have to draw against the subconscious mind, until they eventually reach a wall that cannot be overcome, and they need to let more excess mana accumulate before casting again."
This leads to several interesting points:
For one, a brainless creature can be manipulated, because it wouldn't have a mana shield.
Animals with small brains may or may not be able to resist the strength of a humans thought.
Bonus: You can write in the same effect as a biological process. Living beings naturally store mana, which protects them from the effects of magic. Only rare humans/animals with a specialized gland/thought pattern/manapool can use magic.
It sounds as though you need something that differentiates a living body from other physical things. You could explain this via the flow of fluids (blood, lymph, chyme, gall, various hormones). Another option would be the electrical impulses that are constantly flowing through living bodies. A third option, to get more metaphysical and magical, would be the "spirit" that animates the body interfering with the magic.
Carbon is a quite peculiar atom. It's nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds. Due having 4 electrons of 8 "electron slots" in its outer orbit, it's able to give, receive and even lend (or borrow) its 4 electrons (to get rid of them and empty its orbit) or 4 electrons of another atom/s (to fill its orbit). That lets carbon make a lot of complex structures, like organic molecules.
This peculiarity makes impossible living organisms for being affected by magic (maybe, even this explain why organism are able to cast magic).
Just look about any protein and see an image, they are extremely complex substances, some of them have thousands (I even dare to say almost a million) of atoms. Thas substances, with the addition of some carbohydrates and the vastly famous nucleic acids (AKA: ADN & ARN), are too complex to be manipulated by magic and instead they do magic.
The complexity of this substances make impossible to manipulate them with the mind (just try to imagine their structure) and also channels the magic avoiding its effects.
My magical system has this feature.
The way this is described, in my work, is via souls:
Magical power permeates the natural world, and during gestation, it concentrates in sensate beings. The crystallized magical essence is a soul, and during the lifetime of a person, that soul leaks magical energy. [Magical users] are unique in that their bodies have two specific adaptations which make use of that leakage:
The first is a shield. This shield repels all direct effects. The body of a [magic user] is inviolate from all direct magical alteration by outside forces. It operates as a vestigal, autonomic, form of personal defense, and its energy cannot be used for spellcasting. Or to be more precise, conscious manipulation of magical shielding is somewhere between conscious control of a heartbeat, or breathing, in terms of difficulty. This shield also inflicts countermagical effects on area-based spells in the immediate vicinity of the [magic user].
Further leakage constitutes the aura which can be used for spellcasting by various means.
Because the crystallized mana of a soul is orders of magnitude higher than what is used for spellcasting (e.g. a soul may contain millions or billions of times the mana used by mid-grade spellcraft), using that leaked mana has no negative effects. Though a [magic user] attempting to use higher amounts of mana than what their aura contains may produce a sort of conversion effect, which violently, and lethally, transitions their magical power from the more dense state (soul) to a less dense state (mana). It doesn't end well for them.
Controlling Magic is rare, having it is not
Very few humans have the ability to actually control or use magic in any way or form, but all living things have some magical essence to them , because theyre alive (or the other way around, your choice), and all most people's magic does is counter outside magical forces the same way an immune system eliminates outside invaders , but you dont actually have any control over it manually.
You basically answered your own question: magic is controlled by the mind. Magic might be rare but when you use it against a living creature it's mind changes the magic and dissipates it. This could be an unconscious action based on the simple idea of what the mind thinks is the "right" way for physics to work.
Magic could even be allowed for anyone and everyone, but the gift to turn off their anti-magic thoughts is rare and prevents magic use for the many.
Magic is only for the pure-- by your universes definition. Pick a trait that ypur mage protagonists have or dont have and make that the reason why pr why not something works. Harry potter did mothers love. So did full metal alchemist. Also-- theres a game where those who have killed become annulled. This means theyre no longer affected by magoc. There was a cult that had initiates kill mages to induct them into the cult. The population in that one was a 50 50 divide of mages and nonmages. Also-- dragon age origins had neat ideas on magic-- specifically blood magic.
