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.

See the git reset man page for details.