If your runs are heavy and have "fingers" a nib filer will come in handy, but be VERY careful when using it because the clear coat that has ran on you will take longer to cure than the rest of it. If you try to file it too soon you will run into real problems. Same goes for sanding real heavy runs. If your runs are smooth sanding will be fine there wont be a need to use a file.

If your runs are heavy try the file or you can use 400-600 to carefully knock them down, I would stop right before you become "level" with the rest of the clear and switch to 1000-1500 to work it flat then 2000 to finish it off before you buff it. Smoother/lighter runs I would use 1000 to to work heavier part of the run down switch to 1500 to work it flat and then 2000 to finish it off before buffing.

Just remember to work it down in stages more or less this will save sanding time and the time needed to buff it out as heavy scratches are alot harder to remove. Take your time and save yourself the headache.