m in E=mc² stands for mass, not matter. It's a bit different. Yes sometimes you can create matter from energy (like in particle accelerators), but more generally you have mass.
For example let's take an atom with 1 proton and 1 electron (hydrogen atom) for simplicity. We would expect this atom to have the mass given by the sum of the masses of the components, so we'd like to say something like: m_H = m_e + m_p with m_H the mass of the atom, m_e the mass of the electron and m_p the mass of the proton. Well, it comes out that it's not quite right, because there's the electron-proton bonding energy that reduces the total mass of the system, so it's more like m_H = m_e + m_p - U_ep with U_ep this energy shared between electron and proton.
In general anyway mass can become energy in decays or nuclear reactions (fusion and fissions), while particle accelerators tend to do the opposite, to convert a big amount of (kinetic) energy into mass (or even better, new matter to study).