A technique for adapting an optical navigation device for navigation on a transparent structure such as a glass plate involves establishing a navigation window for navigation tracking, detecting reflected light within the navigation window, generating an output signal in response to the detected light, and adjusting a characteristic of the navigation window in response to the output signal. An optical navigation device includes an illumination system configured to output light, an image sensor configured to generate an output signal related to a detected portion of the light, and a transparent structure adapter module configured to adjust a navigation window of the image sensor in response to the output signal to adapt the optical navigation device for use directly on an opaque surface or for use on a transparent structure that is located between the optical navigation device and the opaque surface.