System and method for correcting a topography of an object being imaged by a multi-array microscope system. The object is forced to conform to a surface of the substrate supporting the object with a suction force and the topography of the chosen object surface is determined. The supporting substrate is bent with the use of force applied to the substrate with at least one actuator such as to reduce the deviations of the determined topography of the object's surface from a pre-determined reference surface by transferring the changes in the curvature of the supporting substrate to the object. In particular, the chosen surface of the object can be substantially flattened for ease of simultaneous imaging of this surface with multiple objectives of the multi-array microscope.