As the digitization of the manufacturing process is accelerating, various data-driven approaches using machine learning are being developed in chemical mechanical polishing (CMP). For a more accurate prediction in contact-based CMP, it is necessary to consider the real-time changing pad surface roughness during polishing. Changes in pad surface roughness result in non-uniformity of the real contact pressure and friction applied to the wafer, which are the main causes of material removal rate variation. In this paper, we predicted the material removal rate based on pressure and surface roughness using a deep neural network (DNN). Reduced peak height (Rpk) and real contact area (RCA) were chosen as the key parameters indicative of the surface roughness of the pad, and 220 data were collected along with the process pressure. The collected data were normalized and separated in a 3 : 1 : 1 ratio to improve the predictive performance of the DNN model. The hyperparameters of the DNN model were optimized through random search techniques and 5 cross-validations. The optimized DNN model predicted the material removal rate with high accuracy in ex-situ CMP. This study is expected to be utilized in data-driven machine learning decision making for cyber-physical CMP systems in the future.