This article proposes a theoretical model of molecular sieving through repeated nanofilter arrays consisting of alternative deep and shallow regions. The role of configurational entropy,which arises from the inaccessibility of some configurations of the molecule in the confined space of nanochannel,is clarified explicitly. It is demonstrated that the configurational entropy difference of anisotropic biomolecules of different sizes dominates the complex partitioning of these molecules over the nanofilter array. In addition,the relationship between the effective mobility and the nanofilter geometries,molecular transport parameters,and the strength of electric fields are described rigorously.As an example,the mobilities for 50,150 and 300 bp DNA molecules are calculated using this model,which matches the experimental data with a error less than 5%. This simplified model allows for fast analysis of nanofilter separation systems,without the need of complicated numerical simulations and physical experiments.