A method of reducing variability of an error associated with a structure on a substrate in a lithography process is disclosed. The method includes determining, based on one or more images obtained based on a scan of the substrate by a scanning electron microscope (SEM), a first error due to a SEM distortion in the image. The method also includes determining, based on the image, a second error associated with a real error of the structure, where the error associated with the structure includes the first error and the second error. A command is generated by a data processor that enables a modification of the lithography process and an associated reduction of the variability of the error based on reducing any of the first error or the second error.