The characteristics of the alignment and misalignment multistage spatial filters are presented in this paper based on their effects on the beam quality. First, the approximate analytical expressions of the modulations of a square beam, which are induced by scatterers and an alignment spatial filter pinhole, are derived. Then, the far field analytical expression of the modulated square beam after its propagation through a nonlinear medium is presented. Subsequently, using a square super Gaussian beam, the modulations induced by an alignment and misalignment spatial filter pinhole are illustrated. The suppressing functions of the alignment and misalignment spatial filters on the hot image are investigated. The effects of the misalignment of the multistage spatial filter pinholes on the output beam quality are studied based on two evaluation factors: fluence beam contrast and fill factor. It is shown that the spatial filter pinhole misalignment has significant influences on both the far field and near field of the downstream beam, especially when nonlinear media exist. The results presented in this paper give important references and guidance for the spatial filter design, installation and alignment.