Molecular imprinting, a common method used in separations and chromatography to isolate specific molecules via surface binding, has been adapted for applications in biomaterials and related sciences. The objective of this study was to determine the effectiveness of different approaches to molecular imprinting by testing for preferential binding of protein on polysiloxane scaffold surfaces. To test preferential rebinding, the scaffolds were exposed to a mixture of the template protein and a competitor protein with similar size but different chemistry. Lysozyme-imprinted polymers rebound 8.13 0.99% of lysozyme without any competition and 5.1 0.3% of the protein during competition. Lysozyme C peptide was imprinted into polysiloxane scaffolds to investigate the epitope approach to molecular imprinting. Without competition, 8.95 11.53% of the lysozyme preferentially bound to the scaffolds, while under competition 1.85 9.47% bound to the scaffolds. Lastly, bone morphogenetic protein 2 (BMP-2) was imprinted into the polymer scaffolds. Results revealed that BMP-2 imprinted scaffolds bound 10.09 6.625% under noncompetitive conditions and a very small 0.65 4.55% during competition. Trends of preferential binding via peptide imprinting and BMP-2 imprinting can be seen, and show promise in future tissue engineering material applications and biomaterial compatibility.