Continuous development in the semiconductor process technology has led to the fabrication of devices with nanometer scale feature resolution. Resonance enhanced atomic force microscopy infrared (AFM-IR) is a novel technique with potential to overcome some limitations of existing tools. This manuscript illustrates chemical characterization of the nanoscale skin and polyester contaminant on silicon wafer using resonance enhanced AFM-IR spectroscopy. Resonance enhanced AFM-IR offers superior sensitivity for nanoscale organic contaminants. To demonstrate this capability, AFM-IR spectra were obtained from contaminants on silicon wafers, and the spectra correlated with a high confidence to a standard transmission FTIR spectral database. In addition, a newly developed high speed spectral acquisition scheme, which augments the reliability of nanoscale defect characterization by reducing the overall data acquisition time and enabling users to perform repeated measurements for statistical analysis, is established.