Since PAN(panchromatic) and MS(multispectral) imagery of pushbroom scanner have the offset between PAN and MS CCD(charge coupled device) in the focal plane, PAN and MS images are acquired at different time and angle. Since clouds are fast moving objects, they should lead mis-registration problem with wrong matching points on clouds. The registration of cloudy imagery to recognize and remove the contamination of clouds can be categorized into three classes: (1) cloud is considered as nose and removed (2) employing multi-spectral imagery (3) using multi-temporal imagery. In this paper, method (1) and (3) are implemented and analysed with cloudy pushbroom scanner images.