In order to remove all files that are currently not under version control by Git from your current working directory, first perform a dry-run:

$ git clean -n -d 
Would remove subdir/a-file.md
Would remove another-file.md

If you’re sure this is the desired result, delete the files for real:

$ git clean -f -d
Removing subdir/a-file.md
Removing another-file.md