External hardisk folders have become shortcut

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Saturday April 27, 2013
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April 27, 2013
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recently couple of days back my 1 tb which i've partioned into two drives got affected by threat "autorun" which had done shortcut to all my folders.Upon friend's advice i tried to run my external drive in linux and could actually see those duplicate link folders so i deleted them..now when i switched back to windows thinking that problem has actually solved but got that it has become more worse than before now my drive doesn't show any folders in windows(i suppose they are hidden) but those folder i can only read in linux ...suggest me solution .