The present disclosure provides methods of fabricating a biochip. The biochip includes a fluidic part, having through-substrate holes as inlets and outlets, and a sensing part bonded together using a bonding material. One or both of the parts has microfluidic channel patterns and one or more patterned surface modification layers formed using different methods to provide surface property for binding bioreceptors and for flowing analytes. The patterning includes lithography, etching, washing, selective depositing using printing or self-assembly of surface chemistry.