In this paper, we investigate optical loss in a free-standing polymer waveguide deflected by mechanical motion. In addition to the propagation loss and the curvature loss, we especially focus on the evaluation of the optomechanical loss, generated by the mechanical bending of the polymer waveguide. For the experimental evaluation of the optomechanical loss, we fabricate three different sets of waveguide test structures for the measurement of propagation loss, curvature loss and mechanical bending loss, respectively. The waveguide structures, fabricated by a 3-mask surface micromachining process, are characterized using a light source of 1330 nm wavelength. The optical loss for each set of test structures has been measured by a photo detector. Then, We obtain an averaged propagation loss of $5.4 \pm 1.1$ dB/cm, a coupling loss of $5.3\pm 2.4$ dB, and a negligible curvature loss from the waveguide, having the curvature radii of 100, 200, 300, 400, 800, 1200, 1600 and $2000 \mu$ m, respectively. From the total optical loss measured from the waveguide bending test, we extract the propagation loss and coupling loss, Thus obtaining the optomechanical loss due to waveguide deflection. The optomechanical loss due to the mechanical deflection is rapidly increased for the deflection beyond elastic region. We also find that the curvature loss and the stress-induced optical property change can be neglected compared to the propagation loss in small deflection region (i.e. elastic deflection region). In large deflection region (i.e. plastic region), however, the optomechanical loss becomes the major portion of the total optical loss of the suspended polymer waveguide.