We demonstrate a simple, controllable, and stable method for fabricating high fill factor cylindrical microlens array with a novel isolated thermal reflow process. In this method, microstripes with a very small gap were obtained via digital micromirror device-based lithography, then covered with polydimethylsiloxane (PDMS) solution. The prepared microstripes were isolated and were heated and reflowed to a cylindrical microlens array. During the reflow process, the semicross-linked PDMS can serve as a barrier to prevent the diameter change and the bonding of adjacent microlenses. By this special treatment, the fill factor of the cylindrical microlens array can be significantly improved. Moreover, the reflow time and temperature have very little effect on the microlens shape due to the surrounded semicross-linked PDMS. This will make our process stabler than traditional methods. The measured 3D profile is good and satisfactory, and excellent optical performance is demonstrated with the fabricated cylindrical microlens arrays. The proposed method may offer a viable route for fabrication of high fill factor microlens arrays in a very simple and stable way.