The present disclosure provides flow cells and methods of fabricating flow cells. The method includes combining three portions: a first substrate, a second substrate, and microfluidic channels between the first substrate and the second substrate having walls of a photoresist dry film. Through-holes for inlet and outlet are formed in the first substrate or the second substrate. Patterned capture sites are stamped on the first substrate and the second substrate by a nanoimprint lithography process. In other embodiments, parts of the patterned capture sites are selectively attached to a surface chemistry pattern formed of silicon oxide islands each disposed on an outcrop of a soft bottom layer.