There are times when you do
git pull or
git pull rebase you get a lots of files that other people contributed that leaves you with lots of untracked files or may be other situation, first thing to try is:
git rest --hard head
If the above does nto help then you can do this
git clean -fd
The above will remove directories as well. Here are some other options that may help.
1) To remove ignored files run:
git clean -f -X or git clean -fX
2) To remove ignored and non-ignored files.
run git clean -f -x or git clean -fx
Git web site has all other option on git-clean.