In the past few decades, many kinds of UAS for image acquisition has been developing. But only high-cost commercial software could be used to image aligning and correcting. This problem caused cost-problem of UAS and complicated for many users. Nowadays, variety of software, not only commercial but also open-source, provides powerful image processing tool. There are so many software to support this processing, but only three popular programs are used to make a comparative study. The goal of this study is to compare the ease of use, overall accuracy and processing time of each software based on chunk of images from UAS.