Constructing multicomponent protein structures that match the complexity of those found in nature is essential for the next generation of medical materials. In this report, a versatile method for precisely arranging multicomponent protein nanopatterns in two-dimensional single-layer or three-dimensional multilayer formats using electron beam lithography is described. Eight-arm poly(ethylene glycol)s (PEGS) were modified at the chain ends with either biotin, maleimide, aminooxy, or nitrilotriacetic acid. Analysis by H-1 NMR spectroscopy revealed that the reactions were efficient and that end-group conversions were 91 - 100%. The polymers were then cross-linked onto Si surfaces using electron beams to form micron-sized patterns of the functional groups. Proteins with biotin binding sites, a free cysteine, an N-terminal alpha-oxoamide, and a histidine tag, respectively, were then incubated with the substrate in aqueous solutions without the addition of any other reagents. By fluorescence microscopy experiments it was determined that proteins reacted site-specifically with the exposed functional groups to form micropatterns. Multicomponent nanoscale protein patterns were then fabricated. Different PEGS with orthogonal reactivities were sequentially patterned on the same chip. Simultaneous assembly of two different proteins from a mixture of the biomolecules formed the multicomponent two-dimensional patterns. Atomic force microscopy demonstrated that nanometer-sized polymer patterns were formed, and fluorescence microscopy demonstrated that side-by-side patterns of the different proteins were obtained. Moreover, multilayer PEG fabrication produced micron- and nanometer-sized patterns of one functional group on top of the other. Precise three-dimensional arrangements of different proteins were then realized.