I have some files in my repository that should be ignored, i added them to the .gitignore but, of course, they are not removed from my repository.

So my question is, is there a magic command or script using filter-branch that can rewrite my history and remove all these files easily? Or simply a command that will create a commit that will remove them ?

You can remove them from the repository manually:

git rm --cached file1 file2 dir/file3

Or, if you have a lot of files:

git rm --cached `git ls-files -i -c --exclude-from=.gitignore`

But this doesn't seem to work in Git Bash on Windows. It produces an error message. The following works better:

git ls-files -i -c --exclude-from=.gitignore | xargs git rm --cached  

In PowerShell on Windows this works even better (handles spaces in path and filenames):

git ls-files -i -c --exclude-from=.gitignore | %{git rm --cached $_}

Regarding rewriting the whole history without these files, I highly doubt there's an automatic way to do it.
And we all know that rewriting the history is bad, don't we? :)