This paper presents a method for non-computationally expensive automatic alignment of cameras that utilises stereoscopic imagery separated at varying distances just below that of the intraocular distance. Here, automatic stereoscopic alignment in real-time is a non-trivial process that relies on calculating the best virtual alignment of camera lenses through image overlaying. This is important as retail 3D camera lenses are typically not sufficiently calibrated for accurate estimates of distance. The alignment of images allows the filtering of background objects and focuses on points of interest. Imprecision in camera lens calibration leads to problems with the required alignment of images and consequent filtering of background objects. The algorithm presented in this paper allows virtual calibration within non-calibrated cameras to provide a real-time filtering of images and the consequent identification of points of interest. The proposed method is capable of generating the best alignment setup at a reasonable computational expense in natural environments with partial background occlusion.