Since this is the thread I found when I searched for information on how to fill holes in terrain, I thought I'd add this tid-bit which may prove useful for new players such as myself:
By default, the mining tool (tool #2) is set to gather only valuable ores. You can also gather non-valuable ores (a.k.a. Soil, Forest Soil, Sand, etc.) by opening the tool interface (select the tool -> open inventory with "i"), then on the top right hand area is a button you can click to enable the gathering of non-valuable ores while you use the tool.
Hope this helps.