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A nanoelectromechanical mass sensor (NEMS) was used to characterize material deposition rates in stencil lithography. The local material deposition on the sensor surface was modeled and compared with the experimental measurements employing the sensor. The model was tested with experimental data obtained by displacing the stencil laterally in a given direction while monitoring the change of resonance frequency of the sensor. Assuming that the change of resonance frequency depends linearly on the deposited mass accretion, the derivative of the change of resonance frequency allows the deposition rate to be spatially resolved. A rectangular aperture with dimensions 20μm (X) by 400μm (Y), located close to the sensor position, was displaced along the X-axis, in the first experiment. In the second experiment, a squared aperture 20μm (X) by 20μm (Y) was displaced along the Y-central axis. The results are found to be in agreement with a purely geometrical modeling of the system.