A new approach to realize multilayer micropatterns with vertical heterostructure is introduced. In this approach, well-defined micropatterns of poly(4-vinylpryridine) (PVP) and poly(acrylic acid) (PAA) multilayer are prepared in short process time by using microfluidic channels combined with the convective self-assembly process (i.e., the self-assembling process in the presence of external flow). The resulting patterns were then used as templates for further spin-coating process of poly(diallyldimethyl ammonium chloride) (PDAC) and poly(sodium 4-styrenesulfonate) (PSS). The micropatterns with sharp edge boundaries and small ridges at the edges were obtained for alternating (PVP/PAA)(5)/(PDAC/PSS)(40) multilayers.