Thermal reflow of polymer to generate spherical profile has been used to fabricate microlenses in this paper. A simple model based on the volume conservation (before and after reflow) and geometrical consideration of lens profile, shows that the focal length of the microlens produced by reflow technique is a function of the initial geometry of microcylinders, i.e. diameter and thickness. This relationship of focal length with diameter and thickness is used as a basis to control focal length. A simple spin coating technique on dual surface is used to achieve differential thickness, to control the focal length of microlenses produced on the same substrate. A biomedical application of such combination of microlenses is endoscopy where the lenses of varying diameter and equal focal length are needed on top of optical fibre bundles to provide independent function of illumination and imaging. This paper incorporates the differential thickness technique to show a micro fabrication process to produce the polymer reflowed microlenses, with a control of focal length based on thickness. The design also helps to integrate these microlenses on top an optical fibre with accurate alignment.