Periodic or gradient subwavelength structures are basic configurations of photonic crystals and metamaterials. While the numerical simulations predict trivial loss, but the fabricated photonic crystal waveguides by E-beam lithography and standard dry etching shows unacceptable loss beyond 10 dB. Nanofabrication variation introduced geometric inhomogeneity is considered as the primary cause of the deleterious performance. The deep UV photolithography in CMOS foundry is a large-scale parallel processing, which can significantly suppress the fabrication-related inhomogeneous offsets and thus the optical linear loss. Here we demonstrate ultra-low loss photonic crystal waveguides with a 300 mm multi-project wafer run. For sub-millimetre long photonic crystal W1 waveguides, consistent performance of 2 dB total loss and 40 dB extinction ratio are observed across different dies.