The analysis of variance for randomized block design or two way classification data is well known. In this paper, particularly, we considered two stage nested design in which the levels of one factor is not identical for different levels of another factor. We investigate the structural properties of two stage nested design and the properties of error sum of squares for random effect model. For the application of two way nested design, we consider two-period crossover design which is used commonly for the equivalence test to bio-similar product. The confidence interval estimation of the difference of two population means in the crossover design is discussed based on statistical package SPSS.