How Fill works
Sinks (and peaks) are often errors due to the resolution of the data or rounding of elevations to the nearest integer value.
Sinks should be filled to ensure proper delineation of basins and streams. If the sinks are not filled, a derived drainage network may be discontinuous.
The Fill tool uses the equivalents of several tools, such as Focal Flow, Flow Direction, Sink, Watershed, and Zonal Fill, to locate and fill sinks. The tool iterates until all sinks within the specified z limit are filled. As sinks are filled, others can be created at the boundaries of the filled areas, which are removed in the next iteration.
The tool can also be used to remove peaks, which are spurious cells with elevation greater than would be expected given the trend of the surrounding surface.
For non-SDTS USGS 30-meter resolution DEMs, Tarboton et al. (1991) found that from 0.9 to 4.7 percent of the cells in a DEM were sinks. The mean adjustment of these sinks ranged from 2.6 to 4.8 meters. This means that for a 1,000 by 1,000 cell grid (1 million cells), there may be 9,000 to 47,000 sinks to be filled. Other DEM data sources may have higher or lower percentages of sinks, depending on how the surfaces were processed.
To fill all sinks whose depth is less than 100 meters, the settings in the Fill tool would be something like the following:
Input surface raster : elevation
Output surface raster : fill_ras1
Z limit : 100
Tarboton, D. G., R. L. Bras, and I. Rodriguez–Iturbe. 1991. "On the Extraction of Channel Networks from Digital Elevation Data." Hydrological Processes 5: 81–100.