Hamed, it's not currently possible to create a timetable that is 3-D (lat-by-lon-by-time). One thing you can do is make a 45*8759x3 timetable, with variables for lat, lon, and temp. Another possibility is to make an 8759x45 timetable with one var for each grid point. Or an 8759x9 timetable each of whose variables is itself 8759x5.
Hard to say which of these might work for you, it depends on what you need to do next.