You can remove tracked files from vcs manually using "Terminal" tab in Android Studio or Git Bash console.
To untrack ignored files you should:
1) Make sure the files you want to ignore are properly listed in .gitignore
2) Commit pending changes (important!)
3) Execute commands
git rm -r --cached .
git add .
4) And then commit again:
git commit -am "Remove ignored files"
These steps will remove all the items from Git Index and then update it again, while respecting git ignores.
The reason for commiting pending changes at step 2 is that if the rm is part of another commit it doesn't work as expected.
Check more information in comments here.