Nylon is a relatively inert polymer. The ability to easily functionalize nylon with biomolecules will improve the utilization of nylon in biological systems. A potential use of the biofunctionalized nylon scaffolds is in devices for cell therapeutics that can specifically select cells present in small numbers, such as hematopoietic stem cells. This study developed a versatile and simple two-step technique combining oxygen plasma treatment with wet silanization to graft biomolecules onto nylon 6,6 3D porous scaffolds. Scaffolds that were exposed to oxygen plasma exhibited up to 13-fold increase in silane attachment ((3-mercaptopropyl)trimethoxysilane/(3-aminopropyl)trimethoxysilane) compared to untreated scaffolds. To address the limitation of nondestructive characterization of the surface chemistry of 3D scaffolds, fluorescent CdSe/ZnS nanoparticles were used as a reporting tool for -NH2 functionalized surfaces. Scaffolds that were covalently bound with neutravidin protein remained stable in phosphate buffered saline up to four months. Functionality of the neutravidin-grafted scaffolds was demonstrated by the specific binding of CD4 cells to the scaffold via CD4-specific antibody. Ultimately, these neutravidin-functionalized 3D nylon scaffolds could be easily customized on demand utilizing a plethora of biotinylated biomolecules (antibodies, enzymes and proteins) to select for specific cell of interest. This technique can be extended to other applications, including the enhancement of cell-scaffold interactions.