matlabのmkdirは新しいフォルダを作成し、そのフォルダに画像を保存します.

for i = 1:size(query_image_index,2)
     mkdir('       \',num2str(query_image_index(i)));       %%                        
     C = imgNamList{query_image_index(i)};
     D = C(1:length(C)-4);
     oriImg = imread(imgNamList{query_image_index(i)});   %              imgNamList       
%      imwrite(oriImg,mkdir('F:\SVM_FCM    \',num2str(query_image_index(i))),D,'.jpg');
     imwrite(oriImg,['       \',num2str(query_image_index(i)),'\',D,'.jpg']);
end