1. A pattern inspecting method used in a pattern inspecting apparatus for inspecting presence/absence of a defect in a fine pattern formed on a transfer mask for lithography, and which irradiates light on a sample to be inspected having a pattern, acquires a pattern image to be inspected by detecting reflection light or transmission light from the sample to be inspected and inspects presence/absence of a defect in a pattern of the sample to be inspected based upon the acquired pattern image to be inspected, the method comprising: performing a pixel positional deviation correction operation, including: superimposing on one another a partial pattern image to be inspected and a partial inspection reference pattern image, said partial pattern image to be inspected obtained by dividing the pattern image to be inspected acquired from the sample to be inspected, said partial inspection reference pattern image obtained by dividing an inspection reference pattern image of the sample to be inspected and corresponding to the partial pattern image to be inspected; correcting a pixel positional deviation between the partial inspection reference pattern image and the partial pattern image to be inspected under such a condition that a sum of squares of level differences between both the partial pattern images becomes minimum; performing a processing for the pixel positional deviation correction on all the partial pattern images to be inspected obtained by the division; collecting pattern image data corrected regarding the pixel positional deviation by regarding the partial inspection reference pattern image corrected regarding the pixel positional deviation and the partial pattern image to be inspected as 2-dimensional input data and 2-dimensional output data, respectively, and scanning the inspection reference pattern image and the pattern image to be inspected in order to set a 2-dimensional input/output linear predictive model having a parameter; performing an identifying operation for identifying the parameter of the 2-dimensional input/output linear predictive model using least-squares method based upon the collected pattern image data; performing a model image operation to obtain a model image corresponding to the partial inspection reference pattern image by a simulation operation using the parameter of the identified 2-dimensional input/output linear predictive model; and performing a comparison operation to compare the model image with the partial pattern image to be inspected to obtain a square error pattern image, to remove noise from the square error pattern image, and to perform a threshold operation processing to specify coordinates of a defective pixel in the partial pattern image to be inspected.