Please don’t use this recipe if your situation is not the one described in the question. This recipe is for fixing a bad merge, and replaying your good commits onto a fixed merge.
Although filter-branch will do what you want, it is quite a complex command and I would probably choose to do this with git rebase. It’s probably a personal preference. filter-branch can do it in a single, slightly more complex command, whereas the rebase solution is performing the equivalent logical operations one step at a time.
Try the following recipe:
# create and check out a temporary branch at the location of the bad merge
git checkout -b tmpfix <sha1-of-merge>
# remove the incorrectly added file
git rm somefile.orig
# commit the amended merge
git commit --amend
# go back to the master branch
git checkout master
# replant the master branch onto the corrected merge
git rebase tmpfix
# delete the temporary branch
git branch -d tmpfix
(Note that you don’t actually need a temporary branch, you can do this with a ‘detached HEAD’, but you need to take a note of the commit id generated by the git commit --amend step to supply to the git rebase command rather than using the temporary branch name.)