In this work, a new method for aerial robot remote sensing using stereo vision is proposed. A variable baseline and flexible configuration stereo setup is achieved by separating the left camera and right camera on two separate quadrotor aerial robots. Monocular cameras, one on each aerial robot, are used as a stereo pair, allowing independent adjustment of the pose of the stereo pair. In contrast to conventional stereo vision where two cameras are fixed, having a flexible configuration system allows a large degree of independence in changing the configuration in accordance with various kinds of applications. Larger baselines can be used for stereo vision of farther away targets while using a vertical stereo configuration in tasks where there would be a loss of horizontal overlap caused by a lack of suitable horizontal configuration. Additionally, a method for the practical use of variable baseline stereo vision is introduced, combining multiple point clouds from multiple stereo baselines. Issues from using an inappropriate baseline, such as estimation error induced by insufficient baseline, and occlusions from using too large a baseline can be avoided with this solution.