A simple and efficient templating method in combination with hot embossing technique is developed for fabricating large-area two-dimensional (2D) microlens arrays (MLAs) with uniform shape. By utilizing a modified microchannel method, a 2D large-area hexagonal close-packed (HCP) array of silica colloidal microspheres is prepared and serves as a template in the following hot embossing treatment to create a polycarbonate (PC) microcavity array. Then, with the obtained PC microcavity structure serving as a mold, a hot embossing process is applied to finally achieve a polymethylmethacrylate (PMMA) MLA. The effect of annealing time during the mold preparation process on the dimensions and shapes of the prepared microlens is investigated. The imaging performances of the prepared PC concave microcavities and PMMA convex microlenses are characterized by carrying out projection experiments. Our method provides a rapid and low cost approach to prepare large-area MLAs.