I tried deleting the files and folder in Modules through FTP...but it won't let me delete the folder saying the folder is not empty even though there is no single file in there.
I know what the problem is I had the same problem till I realised what it was its something to do with .htaccess files try deleteing your .htaccess file from your root folder or rename it temporary.
If you are failing to delete directories with an FTP client, I suspect that you do have hidden files that your FTP client is not showing you that are preventing you from deleting the directories in question. The suggestion of the previous poster that it is an .htaccess file is a pretty good one. Fiddling with your FTP software may help. Trying another FTP program may also help.
If that doesn't work, if you have shell access to your host, you can always ssh to the box and try "rm -Rf ./modules/offending-module-directory". Be very, very, very careful with rm -Rf, though. It's like cutting meat with a chainsaw and you can seriously *beep* up with it if you are not careful.
Another problem is that modules have components all over the place -- in /admin/case, /admin/language, /admin/links, /admin/modules, in /modules, sometimes in /images. Depends on the module where you have to go to get everything.
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