If I understand the question correctly, you simply want to "undo" the
git add that was done for that file.
If you need to remove a single file from the staging area, use
git reset HEAD -- <file>
If you need to remove a whole directory (folder) from the staging area, use
git reset HEAD -- <directoryName>
Your modifications will be kept. When you run
git status the file will once again show up as modified but not yet staged.
git reset man page for details.