Adequate segmentation of target objects from the background plays an important role for the performance of automatic target recognition(ATR) system. This paper presents a new segmentation algorithm using fuzzy thresholding to extract a target. The proposed algorithm consists of two steps. In the first step, the region of interest(ROI) including the target can be automatically selected by the proposed robust method based on the frame difference of each image sensor. In the second step, fuzzy thresholding with a proposed membership function is performed within the only ROI selected in the first step. The proposed membership function is based on the similarity of intensity and the adjacency of target area on each image. Experimental results applied to real CCD/IR images show a good performance and the proposed algorithm is expected to enhance the performance of ATR system using multi-sensors.