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.