A pharmaceutical manufacturing process to produce a preferred isomer was studied using Raman spectroscopy. One of the objectives is to achieve better control throughout the process, as a way for improving product quality. In order to accurately characterize the preferred isomer and undesired isomer during synthesis process, appropriate Raman data pre-treatments are necessary to correct baseline drifts and pathlength variations. Multivariate Curve Resolution (MCR) is applied to monitor relative concentrations of a major reagent and the isomers over time. Principal Component Analysis (PCA) score plots of different batches are useful in the following changes of measured spectra and to study batch-to-batch difference.