We introduce a novel method for correcting distortion in thin silicon substrates caused by coating stress. Thin substrates, such as lightweight mirrors for x-ray or optical imaging, and semiconductor wafers or flat panel substrates, are easily distorted by stress in thin film coatings. We report a new method for correcting stress-induced distortion in flat silicon substrates which utilizes a micro-patterned silicon oxide layer on the back side of the substrate. Due to the excellent lithographic precision of the patterning process, we demonstrate stress compensation control to a precision of ~0.2%. The proposed process is simple and inexpensive due to the relatively large pattern features on the photomask. The correction process has been tested on flat silicon wafers that were distorted by 30 nm-thick compressively-stressed coatings of chromium, achieving RMS surface height and slope error reductions of a factor of 68 and 50, respectively.