As the integration density in the manufacturing of IC's increases and tighter design rules are implemented, the accuracy of overlay in the photolithography process is becoming all the more important. Consequently, investigation and characterization of the accuracy (as well as precision) of the overlay measurement are being required to insure that the overlay metrology tool qualifies for the new technologies. In this paper, we analyze the relationship between wafer substrate types and the respective characteristic overlay measurement errors associated with them. We compare results using different illumination wavelengths in the overlay tool. We define the Wafer Induced Shift (WIS) contribution to the measurement accuracy error and introduce a metric for it. And we analyze the relationship between the TIS and WIS. We show that the wavelength of the optical overlay measurement (OL, for short) should be fitted separately to each of the various kinds of overlay measurement targets, or marks. Buried type targets, covered by transparent materials, for which the measurement is made through the transparent interlayer, benefit from wavelength selection due to the possible improvement in contrast associated with an interference effect. Open type targets, on the other hand, in which the measurement signal is collected off the substrate shape itself, do not benefit from that. There is another problem to consider, however. Such targets may show a considerable WIS, even thought TIS and precision are good both before and after etch. The WIS error can be as high as 100 nm. This could create serious OL problem and it means that TIS and precision are not enough to characterize the quality of measurement, and WIS is equally important, it not more so. We look into the causes of WIS in the substrate shape, overlay mark design and fabrication method. We show that with careful selection of illumination wavelength, some layers produce no WIS. On the other layers WIS remains a problem and other methods are still required to control it.