i deleted a folder from my local Git repository then i committed and pushed the changes to the remote repository, the files are deleted but the folder and the sub folder are sti
Git doesn't actually store directories. It just makes directories wherever it needs them to hold the files that are in the repository. If a new clone still creates those directories, make sure you don't have files you can't see (like .gitignore) present.
You can force git to quit tracking a local file by calling:
git rm file.txt #warning, this also deletes the file from your filesystem
You can delete an entire directory (and it's contents) by calling:
git rm -rf directory