Using a multi-scale approach which combines both molecular dynamics (MD) and kinetic Monte Carlo (KMC) simulations, we study a simple and scalable method for fabricating charge-stabilized nanoparticles through a rapid solvent exchange, i.e., Flash NanoPrecipitation (FNP). This multi-scale approach is based on microscopic information from MD simulations and uses a KMC algorithm to access macroscopic length- and time scales, which allows direct comparison with experiments and quantitative predictions. We find good agreement of our simulation results with the experiments. In addition, the model allows us to understand the aggregation mechanism on both microscopic and macroscopic levels and determine dependence of nanoparticle size on processing parameters such as the mixing rate and the polymer feed concentration. It also provides an estimate for the characteristic growth time of nanoparticles in the FNP process. Our results thus give useful insights into tailoring the FNP technique for fabricating nanoparticles with a specific set of desirable properties for various applications.