there are a few things that can fix this.
to start, what kind of boot is it? give me the make and model.
some boots have a removable footboard, which can (sometimes) be grinded.
when you grind the boot board, you are giving the top of the foot more room at whatever point(s) you grind. In addition to this you can grind the "roof" of the shell, if you know what im saying, with a dremmel.
before this however, i would recommend you ski the boot for like 4-5 full days. This will break in the liner and will give you a few mm of space, which is HUGE when you are talking boot fitting.
hope this helps.