Protein patterning is an essential element to the creation of sensing motifs that rely on receptor-ligand binding for selectivity. Microfluidic devices have the potential to greatly aid in the development of simple, robust methods for deposition of biological capture agents. Here we present the characterization of two methods static microfluidic patterning (sMFP) and flow focused microfluidic patterning (ffMFP), for deposition of biological receptors on a waveguide surface. These focusing techniques are used to create localized regions of immobilized agents onto a SiNx waveguide. The receptor agents increase the cross section of the waveguide core, and thus modify the local evanescent field. Therefore the immobilized patch, as well as any secondary binding events, can be detected by monitoring the change in the localized evanescent field. The impact of different flow types (hydrodynamic versus electrokinetic) and microfluidic material (native versus modified) on immobilization density and spot size will be presented.