The development of three-dimensional architectures in semiconductor technology is paving the way to new device concepts for various applications, from quantum computing to single photon avalanche detectors. In most cases, such structures are achievable only under far-from-equilibrium growth conditions. Controlling the shape and morphology of the growing structures, to meet the strict requirements for an application, is far more complex than in close-to-equilibrium cases. The development of predictive simulation tools can be essential to guide the experiments. A versatile phase-field model for kinetic crystal growth is presented and applied to the prototypical case of Ge/Si vertical microcrystals grown on deeply patterned Si substrates. These structures, under development for innovative optoelectronic applications, are characterized by a complex three-dimensional set of facets essentially driven by facet competition. First, the parameters describing the kinetics on the surface of Si and Ge are fitted on a small set of experimental results. To this goal, Si vertical microcrystals have been grown, while for Ge the fitting parameters have been obtained from data from the literature. Once calibrated, the predictive capabilities of the model are demonstrated and exploited for investigating new pattern geometries and crystal morphologies, offering a guideline for the design of new 3D heterostructures. The reported methodology is intended to be a general approach for investigating faceted growth under far-from-equilibrium conditions.