We present in this work the fabrication of high aspect ratio nanopores in 500 nm PECVD SiC films through AAO (anodic aluminum oxide) mask. The initial AAO thin film is 180 nm thick and the diameter of nanopores is 33 ± 7 nm. We have used three plasma chemistries: CF4, Cl2 /Ar, and SF6/O2 to study the pattern transfer process into SiC at sub-50 nm scale by deep reactive ion etching. CF4 and Cl2/Ar etchings show highly anisotropic features. Vertical pores with similar diameter as the AAO mask (33 ± 12 nm) and as deep as 400 nm (aspect ratio > 10) can be achieved by CF4 reactant. As comparison, SF6 /O2 chemistry generates very different etching profiles, causing trenches both in vertical and lateral directions. Our PECVD SiC nanopores are promising candidates for robust biosensing and nanofiltration applications.