Microlens arrays with specially required micropatterns are highly desirable for digital optical processors, microimaging systems, optical photolithography as well as various biomedical imaging and detecting applications. However, realization of such devices efficiently remains technically challenging. Here, a facile and efficient route for large-area microlens arrays (MLAs) with programmable micropatterns is demonstrated. The fabrication process involves a femtosecond laser wet etch process combined with the replication process of hot embossing. Special arranged microlens arrays, including a doublet microlens array, a three-microlens group array, a four-microlens group array, and a six-petallike microlens array as examples, were fabricated by this method. The fabricated MLAs exhibit excellent surface morphology quality and optical imaging properties. This presented technique provides an efficient way to flexibly design the size, shape and the arrangement of the MLAs by adjusting the process parameters such as the pulse energy, the number of shots etching time and the distribution of ablation-induced craters and Programming arrangement.