Merge a branch into new one (squash) and remove the files not needed:
git checkout master
git checkout -b <branch>
git merge --squash <source-branch-with-many-commits>
git reset HEAD <not-needed-file-1>
git checkout -- <not-needed-file-1>
git reset HEAD <not-needed-file-2>
git checkout -- <not-needed-file-2>
git commit