We describe a robust and facile approach to the selective modification of patterned porous films via layer-by-layer (LBL) self-assembly. Positively charged honeycomb-patterned films were prepared from polystyrene-block-poly(N,N-dimethyl-aminoethyl methacrylate) (PS-b-PDMAEMA) and a PS/PDMAEMA blend by the breath figure method followed by surface quaternization. Alginate and chitosan were alternately deposited on the films viaLBL self-assembly. The assembly on the PS-b-PDMAEMA film exhibits two stages with different growth rates, as elucidated by water contact angles, fluorescence microscopy, and quartz crystal microbalance results. The assembly can be controlled on the top surface or across all surfaces of the film by changing the number of deposition cycles. We confirm that there exists a Cassie–Wenzel transition with an increase in deposition cycles, which is responsible for the tunable assembly. For the PS/PDMAEMA film, the pores can be completely wetted and the polyelectrolytes selectively assemble inside the pores, instead of on the top surface. The controllable selective assembly forms unique hierarchical structures and opens a new route for surface modification of patterned porous films.