This paper demonstrates integration of three Fabry-Perot filter stacks on top of a commercially available CMOS image sensor (CIS) for hyperspectral imaging applications. This compact line scan hyperspectral imager fabricated in a 200 mm CMOS process line has 96 bands in the 450–900 nm wavelength range, hence, covering both visible (VIS) and near infrared (NIR) wavelength range. Three independent filter banks (FB) with well-tuned cavity steps provide good spectral performance within their defined range. A common cavity etch of all three FBs is performed by a sequence of lithography and wet etch steps to create a staircase-like structure in which each step acts as an independent filter. To efficiently pattern multiple complex filter stacks, mask design is adopted in such a way that the filters are etched only on flat areas, covering and leaving the area with high topography unchanged.