Real-time control by multiwavelength phase-modulated ellipsometry (PME) of the growth of multilayer structures deposited on transparent glass is presented. The structures consist of plasma-deposited SiO(2) and SiN(x) stacks. A model that takes into account incoherent reflection in the substrate is described and tested. A generalized feedback control method that incorporates the incoherent modeling of the transparent substrate is further applied to the growth of a Fabry-Perot and a standard quarter-wave filter. The resulting optical coatings characterized by spectroscopic PME and transmission measurements show a reproducible precision, with less than 1% error between target and measured spectral responses.