Methods and systems for detecting a particle defect on a wafer surface, transforming the particle to a spectroscopically active state, and identifying a material composition of the activated particle by a spectroscopic technique are described herein. Particle defects are transformed by chemical treatment, thermal treatment, photochemical treatment, or a combination thereof, such that an activated particle exhibits atomic vibrational bands that can be observed spectroscopically. In one embodiment, a surface inspection system detects the presence of a particle defect on a wafer surface, activates observable Raman bands in one or more of the detected particles, and identifies the material composition of the activated particle by a spectroscopic technique. By performing both defect detection and composition analysis on the same inspection tool, it is not necessary to transfer a wafer to a different review tool, or combination of tools, to perform composition analysis of particle defects deposited on semiconductor wafers.