An analytical system is presented that is used to take measurements of objects perceived in stereo image pairs obtained from a scanning electron microscope (SEM). Our system operates by presenting a single stereo view that contains stereo image data obtained from the SEM, along with geometric representations of two types of virtual measurement instruments, a ''protractor'' and a ''caliper''. The measurements obtained from this system are an integral part of a medical study evaluating surfactant, a liquid coating the inner surface of the lung which makes possible the process of breathing. Measurements of the curvature and contact angle of submicron diameter droplets of a fluorocarbon deposited on the surface of airways are performed in order to determine surface tension of the air/liquid interface. This approach has been extended to a microscopic level from the techniques of traditional surface science by measuring submicrometer rather than millimeter diameter droplets, as well as the lengths and curvature of cilia responsible for movement of the surfactant, the airway's protective liquid blanket. An earlier implementation of this approach for taking angle measurements from objects perceived in stereo image pairs using a virtual protractor is extended in this paper to include distance measurements and to use a unified view model. The system is built around a unified view model that is derived from microscope-specific parameters, such as focal length, visible area and magnification. The unified view model ensures that the underlying view models and resultant binocular parallax cues are consistent between synthetic and acquired imagery. When the view models are consistent, it is possible to take measurements of features that are not constrained to lie within the projection plane. The system is first calibrated using non-clinical data of known size and resolution. Using the SEM, stereo image pairs of grids and spheres of known resolution are created to calibrate the measurement system. After calibration, the system is used to take distance and angle measurements of clinical specimens.