Many applications require the ability to image a scene in several different narrow spectral bands simultaneously. Conventional multi-layer dielectric filters require control of film thickness to change the resonant wavelength. This makes it difficult to fabricate a mosaic of multiple narrow spectral band transmission filters monolithically. We adjusted the spectral transmission of a multi-layer dielectric filter by drilling a periodic array of subwavelength holes through the stack. Multi-band photonic crystal filters were modeled and optimized for a specific case of filtering six optical bands on a single substrate. Numerical simulations showed that there exists a particular air hole periodicity which maximizes the minimum hole diameter. Specifically for a stack of SiO2 and Si3N4 with the set of filtered wavelengths (nm): 560, 576, 600, 630, 650, and 660, the optimal hole periodicity was 282 nm. This resulted in a minimum hole diameter of 90 nm and a maximum diameter of 226 nm. Realistic fabrication tolerances were considered such as dielectric layer thickness and refractive index fluctuations, as well as vertical air hole taper. Our results provide a reproducible methodology for similar multi-band monolithic filters in either the optical or infrared regimes.