A spectroscopic ellipsometry (SE) model was developed and implemented to study substrate loss in shallow implanted silicon (i-Si) substrates following a photoresist strip. The model is based on different optical properties of silicon dioxide (SiO2) and i-Si layers and silicon substrates and is used to characterize relevant layers, i-Si and SiO2, before and after plasma treatment. An increase in SiO2 and a decrease in the i-Si layer were observed after plasma exposure. Changes in the i-Si layer are the result of two phenomena, oxidation and heating-induced regrowth of the i-Si layer, while changes in the SiO2 thickness represent the direct measure of substrate loss due to oxidation. Transmission electron microscopy (TEM) and secondary-ion mass spectrometry (SIMS) analysis were performed to cross-check the validity and accuracy of the SE model. The TEM results confirm that the SE model can distinguish between a crystalline (c-Si) substrate and an i-Si layer regardless if the i-Si is damaged, crystalline, or amorphized. There is also good consistency between the SE and SIMS results. For the plasma processes studied in this work, minimal changes in layer thicknesses and substrate losses measured by SE agree very well with the measured SIMS dopant profiles.