The article describes the multifunctionality of a novel black silicon (BS) nanostructured surface covered with a thin layer of noble metal prepared in the a microfluidic channel. It is focused on the separation properties of the BS substrate with direct detection of the separated analytes utilizing surface enhanced Raman spectroscopy. The same BS substrate is providing the stationary phase and a surface enhancement of the Raman signal that has been measured previously to be around 10. As tested molecules, the common components of explosives 1,3 dinitrobenzene and 2,4 dinitrotoluene were used. The separation of selected molecules was achieved with the dried toluene as a mobile phase in a 25 micrometers deep, 5 mm wide, and 4 cm long microfluidic channel during the 2 min. Copyright © 2012 John Wiley & Sons, Ltd.