The current miniaturization trend in the market of inertial microsystems is leading to movable device parts with sizes comparable to the characteristic length-scale of the polycrystalline silicon film morphology. The relevant output of micro electro-mechanical systems (MEMS) is thus more and more affected by a scattering, induced by features resulting from the micro-fabrication process. We recently proposed an on-chip testing device, specifically designed to enhance the aforementioned scattering in compliance with fabrication constraints. We proved that the experimentally measured scattering cannot be described by allowing only for the morphology-affected mechanical properties of the silicon films, and etch defects must be properly accounted for too. In this work, we discuss a fully stochastic framework allowing for the local fluctuations of the stiffness and of the etch-affected geometry of the silicon film. The provided semi-analytical solution is shown to catch efficiently the measured scattering in the C-V plots collected through the test structure. This approach opens up the possibility to learn on-line specific features of the devices, and to reduce the time required for their calibration.