Vertical integration of device layers is a prevailing strategy to boost the performance of microchips and optical devices while maintaining a small form factor. In this paper, we introduce light blocking optical alignment rulers (LBOARs) for layer-by-layer alignment of thin films, which can be potentially applied in manufacturing three-dimensional integrated circuits. LBOAR measures the blocking of the light transmitted through two vertically stacked subwavelength aperture arrays (gratings), which are fabricated onto the separate device layers to be aligned. Here, detailed numerical studies and proof-of-concept experiments on LBOAR are presented. The simulation results reveal two different mechanisms governing the light transmission through a pair of rulers: light blocking and induced extraordinary optical transmission (EOT). In the light-blocking regime, the intensity change is very sensitive to the horizontal shift between two rulers. In contrast, EOT-based alignment is significantly disturbed by the vertical separation of the nearly contacting rulers. Therefore, LBOAR can be more advantageous than EOT-based alignment for certain applications that require only horizontal alignment between two layers of devices. To validate the light-blocking concepts, in our experiments, two-layer stacked LBOARs were fabricated using laser lithography, physical vapor deposition, and dry etching. Optical transmission measurements show that in the nearly perfect alignment condition the transmitted intensity in the light-blocking regime drops significantly providing an alignment accuracy better than 200 nm.