1. A method for providing a coarse alignment between a first image signal and a second image signal for a substrate on an x/y stage of an inspection machine defining x and y directions, said inspection machine having a fixed pixel size and pixel grid that is correlated to positions of said x/y stage, for each selected x position in the x direction during scanning of said substrate, said substrate in the y direction, said coarse alignment method comprising the steps of: a. storing a first swath signal of said first image signal in a first memory; b. determining x and y position coordinates in the x and y directions, respectively, of a first pixel of said first swath signal of said first image signal of step a. relative to boundaries of a pixel of said pixel grid; c. scanning across a first pattern on said substrate to determine a first swath signal of said second image signal; d. determining x and y position coordinates of a first pixel of said first swath signal of said second image signal detected in step c. relative to the boundaries of a pixel of said pixel grid in which said first pixel of said first swath of said second image signal is detected; e. calculating the positional offset of said x and y coordinates of said first pixel of said first swath of said second image signal within said pixel of said pixel grid of step d. from said x and y coordinates of said first pixel of said first image signal within said pixel of said pixel grid from step b.; and f. performing a running alignment of said first pixel of each swath signal of said second image signal within said pixel grid in relation to said first pixel of said first image signal using said positional offset calculated in step e. by advancing or retarding said x path to correct for said x positional offset, and advancing or retarding the scan in the y direction to correct for said y positional offset to realign each swath signal of said second image signal with each swath signal of said first image signal.