Changing the magnification will directly affect the accuracy of the result you're going to achieve. In some cases, the entire measurement process can be done at a single magnification level, however it is quite common that the level of magnification be changed depending on the feature type, size and accuracy requirements. PC-DMIS Vision makes adjustments to accommodate changes in magnification.
Focus accuracy is particularly affected by magnification. Higher magnification allows you to obtain higher focus accuracy. Measurements in Z are almost always done at the highest level of magnification.
Magnification is calibrated through "Field of View Calibration" and adjusted for optimal measurement of your feature via the "Probe Toolbox: Magnification tab".