The performance of polycrystalline thin film CdTe solar cells is limited by as yet poorly understood deep level defects which serve as recombination centers. Electron paramagnetic resonance (EPR) has unrivaled analytical power and sensitivity in the identification of deep level defects in semiconductors; however, very little EPR literature exists with regard to technologically relevant processing of present day polycrystalline CdTe solar cells. In this study we explore the effects of several features important in these present day processing techniques: (1) effects of CdCl2 etching and (2) effects of Cu on the CdTe. Cu is widely used with CdTe solar cells and is thought to play a significant role in CdTe solar cells performance. Although the EPR spectra in all the cases we explored are dominated by a substitutional Mn site signal, our results are clearly sensitive to multiple changes caused by the aforementioned processing parameters.