Anisotropic Flow, an anisotropy of the azimuthal distribution of emitted particles in momentum space with respect to the reaction plane, is a sensitive tool to study the early stage of high energy heavy ion collisions at RHIC. It is commonly studied by measuring the Fourier harmonics ($v_n$) of this distribution. Elliptic flow ($v_2$) in Au+Au collisions is well studied at RHIC and is thought to reflect conditions from the early stage of the collision. We will present the results of $v_2$ and $v_4$ for inclusive charged hadrons as well as identified particles in $\sqrt{s_{NN}}$ = 200 GeV Cu+Cu and Au+Au collisions at PHENIX and discuss the scaling properties of $v_2$ and $v_4$ and the system size dependence of anisotropic flow. We will also report and discuss the results of $v_2$ for identified hadrons in higher $p_T$ region measured by Aerogel counter in Au+Au collision.