The Multi-level 3D (M3D) project simulatesplasmas using multiple levels of physics, geometry and grid modelsin one code package. The M3D code has been extended to fundamentally non-axisymmetric and small aspect ratio, R/a >~1, configurations.Applications include the non-linear stability of the NSTX spherical torus and of the spherical pinch, as well as the relaxation of stellaratorequilibria. The fluid level physics model has been extended to evolve theanisotropic pressures pj|| and pj⊥ for the ion and electron species and has been applied to magnetic island evolution.