We present numerical methods to enable accurate and robust level-set based simulation of anisotropic wet etching and non-planar epitaxy for semiconductor fabrication. These fabrication techniques are characterized by highly crystal orientation-dependent etch/growth rates, which lead to non-convex Hamiltonians in their description by the level-set equation. As a consequence, instable surface propagation may emerge, leading to unphysical results. We propose a calibration-free Stencil Lax-Friedrichs scheme and an advanced adaptive time-stepping approach, tailored to the level-set speed functions associated with anisotropic etching and epitaxy. The scheme calculates the numerical dissipation based on information about the local geometry and the nature of the etch rates/growth function, which enables an optimized tradeoff between overly rounding of sharp geometric features and stable surface propagation. Furthermore, we introduce the deposition top layer method, which allows for robust handling of multiple material regions in non-planar epitaxy simulations. Both methods are demonstrated in a prototypical implementation, which is used to validate the capability and accuracy of our approaches. In particular, two-dimensional wet etching and three-dimensional epitaxy simulations are performed and characteristic geometry parameters are compared to the ideally expected values, showing robustness and high accuracy.