A nanoelectromechanical mass sensor is used to characterize material deposition rates in stencil lithography. The material flux through micron size apertures is mapped with high spatial (below 1 μm) and deposition rate (below 10 pm/s) resolutions by displacing the stencil apertures over the sensor. The sensor is based on a resonating metallic beam (with submicron size width and thickness) monolithically integrated with a CMOS circuit, resulting in a CMOS/NEMS self-oscillator. The sensor is used to test alignment for multi-level nanostencil lithography.