Using a surface forces apparatus (SFA), we quantitatively study the influence of surface damage on the contact mechanics of self-mated glassy polystyrene (PS) films. We use the SFA to measure the contact radius, surface profile, and normal force between the films, including the adhesion force. The molecular weight (MW) of the polymer influences the repeatability of the adhesion measurements and the effective surface energy calculated using the Johnson-Kendall-Roberts (JKR) theory. For low-MW PS (MW = 2.33 kDa), the effective surface energy increases over repeated adhesion cycles as the films become progressively damaged. For high-MW PS (MW = 280 kDa), the effective surface energy is constant over repeated adhesion cycles, but hysteresis is still present, manifested in a smaller contact radius during compression of the surfaces than during separation. Our results demonstrate that while the JKR theory is appropriate for describing the contact mechanics of glassy polymer thin films on layered elastic substrates, the contact mechanics of low-MW polymer films can be complicated by surface damage to the films.