We report ultra-compact surface-normal high-Q optical filters based on single- and double-layer stacked Fano resonance photonic crystal slabs on both Si and quartz substrates. A single layer photonic crystal filter was designed and a Q factor of 1,737 was obtained with 23 dB extinction ratio. With stacked double-layer photonic crystal configuration, the optical filter Q can increase to over 10,000,000 in design. Double-layer filters with quality factor of 9,734 and extinction ratio of 8 dB were experimentally demonstrated, for a filter design with target Q of 22,000.