Turn a jam chuck (JC), put the open end of the box bottom on the JC, and with a freshly sharpened spindle gouge or round scraper, carefully and with a light touch remove the nub.
By that I mean that his solution is one of the two ways to solve the problem. The other is to carefully part off the box, use a knife or chisel to carve away the nub, and then sand the bottom, either manually or with a sanding mandrel mounted in you scroll chuck.
do you mean the base of the box that sits down onto the surface its placed on? or the inside of the box?
I prefer to jam chuck the base of the box to remove the chuck tenon and finish it, its also best to cut it slightly concave so that it guarantee's it will always sit flat.
for inside the box a little "pip" in the centre is very common and the easiest way i have found to remove it is with a round nose negative rake scraper
There are a few choices. A scraper works as Louie recommended. This is also a good use for a carbide tool, either round or Radius square. The other choice for a larger diameter box is a bowl gouge sharpened to a more blunt angle, sometimes called a bottom feeder. This lets you still rub bevel while making the cut leaving a very clean surface.