Optical color filters are widely applied in many areas including display, imaging, sensing, holography, energy harvest, and measurement. Traditional dye-based color filters have drawbacks such as environmental hazards and instability under high temperature and ultraviolet radiation. With advances in nanotechnology, structural color filters, which are based on the interaction of light with designed nanostructures, are able to overcome the drawbacks. Also, it is possible to fabricate structural color filters using standard complementary metal-oxide-semiconductor (CMOS) fabrication facilities with low cost and high volume. In this work, metasurface-based subtractive color filters (SCFs) are demonstrated on 12-inch (300-mm) glass wafers using a CMOS-compatible fabrication process. In order to make the transmissive-type SCF on a transparent glass wafer, an in-house developed layer transfer process is used to solve the glass wafer handling issue in fabrication tools. Three different heights of embedded silicon nanopillars (110, 170, and 230 nm) are found to support magnetic dipole resonances. With pillar height and pitch variation, SCFs with different displayed colors are achieved. Based on the resonance wavelength, the displayed color of the metasurface is verified within the red-yellow-blue color wheel. The simulation and measurement results are compared and discussed. The work provides an alternative design for high efficiency color filters on a CMOS-compatible platform, and paves the way towards mass-producible large-area metasurfaces.