Just unscrew and remove those standoffs that do not line up with the holes in your MB. Relocate the standoffs as needed to line up with MB mounting holes. Most computer cases come with extra threaded holes where you can install a standoff.
Most of us like to have a standoff in each hole location, but sometimes one or two will be missing. Just be sure that there are no standoffs sticking up under you MB that do not have a corresponding MB mounting hole. Short circuits are bad juju.