Spotlight and All My Files can be a real time saver tool on mac but if you are a developer with lots of junk scripts within your project that can go messy. luckily we are able to exclude folders and files in spotlight privacy settings, but adding them to the privacy section will not immediately remove them from spotlight index.
The solution to this is to manually force spotlight to rebuild the index by executing following command in terminal:
sudo mdutil -E /
running this alone is not enough tough. make sure you restart your mac and it should help with spotlight respecting your privacy setting.