Fouling of surfaces is often problematic in microfluidic devices, particularly when using protein or -enzymatic solutions. Various coating methods have been investigated to reduce the tendency for protein molecules to adsorb, mostly relying on hydrophobic surface chemistry or the antifouling ability of -polyethylene glycol. Here we present the potential use of superhydrophobic surfaces to not only reduce the amount of surface contamination but also to induce self-cleaning under flow conditions. The methodology is presented in order to prepare superhydrophobic surface coatings having micro- and nanoscale feature dimensions, as well as a step-by-step guide to quantify adsorbed protein down to nanogram levels. The fabrication of these surfaces as coatings via silica sol-gel and copper nano-hair growth is presented, which can be applied within microfluidic devices manufactured from various materials.