As device size is going under the sub-60 nanometer scale, lithography is facing its resolution limit. To solve this resolution limit it has been suggested that one critical device layer could be made from multi photo/etch process, which needs tighter overlay and critical dimension (CD) controls than normal single exposure process. For CD control in this multi photo/etch process, the problem is that we do not know which pattern is made from which photo/etch process after final process. This makes it impossible to measure the specific process pattern's CD independently. In this case the conventional CD measuring method, which measures multi CDs in FOV(Field Of View) of SEM(Scanning Electronic Microscope) and control their average and distribution, couldn't know the average difference between both patterns because the variance from simply measured multi CD is just sum of each variance and their cross terms not including the average difference. In this paper it is pointed out the statistical problem of classical multi CD measurement in the indistinguishable multi-process pattern and a compensative method is suggested with a new statistical formula.