This paper investigates the question of whether optimization of the conditioning sweep schedule on a commercial rotary polishing tool to produce and maintain the flattest possible macroscopic pad surface can produce, as a side effect, significant changes in pad microscopic surface topography. We first condition a pad to steady state using a sinusoidal sweep and a well-characterized conditioner and measure both the macroscopic pad thickness profile and the microscopic topography at several radii. Tool operational parameters and conditioner data are then used in a pad conditioning model to successfully match the measured macroscopic pad thickness profile. We find in matching the profile that the subpad elastic modulus significantly affects the predicted pad thickness variation. After using the model to optimize the conditioning sweep, we then repeat the steady state conditioning experiment to verify that the pad meets flatness expectations and measure changes in the microscopic surface texture.